title: THP1_PMA48_rep2_ATACseq

description: ATACseq

extract_protocol:
For THP1 cells, cells were stained with a final concentration of 1 ng/ml DAPI in growth media, and 200,000 live cells were sorted using a BD FACSAria and placed on ice. 50,000 cells were then processed using the Active Motif ATACseq kit (cat. 53150).
For THP1 cells, libraries were constructed using the dual index barcodes included in the Active Motif ATAC-seq kit (cat. 53150), except that after the PCR amplification, libraries were size selected with 1.5X SPRI beads instead of 1.2X SPRI beads in order to retain smaller fragments. Libraries were then quantified using Qubit and Bioanalyzer analysis, pooled, and sequenced using an Illumina NextSeq 500.

value: PMA 100nM


title: iPS253-RPE, 6 weeks, rep1, cell5

status: Public on May 04 2024

type: SRA

city: Suita

first: Katsuyuki

last: Shiroguchi

state: Osaka

address: 6-2-3 Furuedai

department: Center for Biosystems Dynamics Research (BDR)

country: Japan

institute: RIKEN

library_source: transcriptomic

data_processing:
Basecalls performed by Illumina Hiseq
Sequenced reads were trimmed for adaptor sequence, and were sorted by indexes using bcl2fastq
Reads were aligned to the gh38 genome assebly using STAR
Mapped reads seperated by genes, and the reads mapped for each gene were clusterd by molecular barcode
The number of cluteres for each gene was counted, which provides the number of molecules detected for each gene
Assembly: gh38
Supplementary files format and content: The calculated copy number of RNA moelcules per cell for each gene is listed.

molecule: total RNA

organism: Homo sapiens

source_name: iPSC derived RPE cell

extract_protocol:
RNAs from cell lysate in each well was directly used for library preparation without purification
Libraries were prepared by using molecular barcoding technique. First, for control, the same amount of spike-in RNAs, a known number of External RNA Controls Consortium (ERCC) RNA molecules, was added into every tube which contains an isolated cell. Then, the cells were lysed and RNA molecules were fragmentated by temperature elevation. cDNAs were generated by reverse transcription using a reverse transcription primer, in which the first common primer sequence, molecular barcode, fourteen T bases, and one V (A or G or C) base are tandemly arranged from 5' end. In the reverse transcription, the second common primer sequence was also attached to 3' end of each generated cDNA molecule by template switching. Subsequently, cDNAs were amplified by PCR using two primers; one primer contains an illumina adapter sequence, sample index, and the first common primer sequence, and the other primer has another illumina adapter sequence, sample index, and the second common primer sequence.

treatment_protocol: Single cells were isolated in wells respectively using Automated Live imaging and cell Picking System (ALPS)

tag: tissue

value: iPSC derived RPE cell

tag: cell line

tag: cell type

value: RPE

tag: rpe culture_period

value: 6 weeks


title: SET-2, WT, DMSO, GFI1B, Rep2

city: Cambridge

first: Brian

last: Liau

state: MA

address: 12 Oxford St.

department: Department of Chemistry and Chemical Biology

country: USA

institute: Harvard University

library_source: genomic

data_processing:
Paired-end reads were aligned to the GRCh38 human reference using the STAR (version 2.7.0e) aligner with splicing disabled.
The resulting .bam file is duplicate-marked and down-sampled to comparable coverage using picard (version 2.22.3).
Peaks for each replicate were called separately with HOMER (version 4.10) with matched inputs before establishing the final peak list with an irreproducible discovery rate (IDR) of 2%.
Replicates were then merged and converted into bigwig files for visualization and quantification with deepTools2
Assembly: hg38
Supplementary files format and content: bigWig and/or bed (except for Input sample)

molecule: genomic DNA

extract_protocol:
SET-2 cells were fixed in 1% formaldehyde, washed, snap frozen, and stored at -80ºC. Sonication of crosslinked cells was calibrated such that DNA was sheared to between 300bp and 2000bp.
ChIP DNA was used to generate sequencing libraries by end repair (End-It DNA repair kit, Epicentre), 3’ A base overhang addition via Klenow fragment (NEB), and ligation of barcoded sequencing adapters.

treatment_protocol: Cells were seeded at 300,000 cells/ml and then treated with vehicle (0.1% DMSO) or 100 nM GSK-LSD1 for the specified time.

value: acute myeloid leukemia

tag: genotype

value: WT

tag: treatment

value: Vehicle

tag: chip antibody

value: Anti-GFI-1B, Santa Cruz, sc-28356


title: THP1_PMA48_rep1_ATACseq

last: Do

address: 500 Main St

department: Biology

institute: MIT

description: ATACseq

data_processing:
Mouse and human data were trimmed using Cutadapt (v3.4) (with parameters -m 20 -q 20 -a CTGTCTCTTATA -A CTGTCTCTTATA), then aligned to the mm10 and hg38 genomes with Bowtie2 v2.4.2 (with parameters --dovetail -I 10 -X 1000 --very-sensitive).
Reads in the mitochondrial genome and unannotated chromosomes as well as the UCSC blacklist were removed, then duplicates were removed with samtools markdup (v1.1.2), and the insert size distribution was calculated using Picard CollectInsertSizeMetrics (v2.25.2) and validated to contain nucleosomal peaks. BED file was then constructed with each mate pair as a separate read using bedtools bamtobed (v2.3.0), and peaks were called using MACS2 callpeak (v2.2.7.1) (with parameters --nomodel --shift -100 --extsize 200 --keep-dup all --call-summits). Note that the MACS2 command shifts each read by 100 base pairs towards the 5’ end and extends the read length to 200 base pairs, thus treating the 5’ end of the original read (the Tn5 cut site) as the center of a new “fragment” that is then used for peak calling and other downstream analysis.
To normalize tracks, reads overlapping shared peaks were counted for each BAM file using featureCounts (with parameters -M -O) and normalization factors were calculated from these counts using the calcNormFactors function in the edgeR package (v3.32.1) in R. Visualization was performed using the bedGraphToBigWig utility and the igv-jupyter package in Python.
Genome_build: hg38
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files for each sample

source_name: THP1 human AML cells

growth_protocol: Cells were grown in RPMI (Corning, 15-040-CV) with 10% dialyzed fetal bovine serum (Sigma, F0392), 4mM glutamine, and 1% penicillin/streptomycin (Corning, 45000-652).

tag: time point


title: YAP-S127A2

city: shanghai

first: Xialu

last: Hong

state: State...

address: 415 Fengyang Road

country: China

institute: Changzheng hospital

data_processing:
The raw reads were filtered by Seqtk before mapping to genome using Hisat2 (version:2.0.4).
. The fragments of genes were counted using stringtie(v1.3.3b) followed by TMM (trimmed mean of M values) normalization
Significant differential expressed genes (DEGs) were identified as those with a False Discovery Rate (FDR) value above the threshold (Q< 0.05) and fold-change >2 using edgeR software.
Assembly: GRCm38.p4 (mm10)
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

organism: Mus musculus

source_name: liver

extract_protocol:
Total RNA was extracted by customer following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 2100 Bioanalyzer (Agilent technologies, Santa Clara, CA, US).Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter,Inc.Kraemer Boulevard Brea, CA,USA)and RNase-Free DNase Set  (Cat#79254, QIAGEN, GmBH, Germany)
According to the instructions of the experiment, the purified Total RNA was separated into mRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.

value: liver

value: hepatocyte

value: 15-week old


title: iPS253-RPE, 6 weeks, rep1, cell6


title: THP1_PMA24_rep2_ATACseq

description: ATACseq


title: iPS253-RPE, 6 weeks, rep1, cell3


title: YAP-S127A1


title: THP1_PMA24_rep1_ATACseq

description: ATACseq


title: SET-2, WT, DMSO, GFI1B, Rep1


title: NC2


title: SET-2, WT, GSKLSD1, LSD1, Rep2

value: Anti-BHC110/LSD1, Bethyl, A300-215


title: SET-2, WT, DMSO, H3K27ac, Rep1

value: Anti-H3K27ac, Active Motif, 39133


title: iPS253-RPE, 6 weeks, rep1, cell2


title: THP1_BRQ48_rep2_ATACseq

description: ATACseq

value: Brequinar 500nM


title: iPS253-RPE, 6 weeks, rep1, cell1


title: SET-2, WT, GSKLSD1, LSD1, Rep1


title: MIM4

city: Rehovot

first: Steffen

last: Jung

address: 234 Herzl Street

department: Department of Immunology

country: Israel

institute: Weizmann Institute of Science

data_processing:
Data analysis was performed using the UTAP transcriptome analysis pipeline 78.Raw reads were trimmed using cutadapt with the parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -a ‘‘A–times 2 -u 3 -u 3 -q 20 -m 25). Reads were mapped to the genome (mm10, Gencode annotation version 10.0) using STAR (v2.4.2a) with the parameters –alignEndsType EndToEnd, –outFilterMismatchNoverLmax 0.05, –twopassMode Basic, –alignSoftClipAtReferenceEnds No. The pipeline quantifies the 30 of Gencode annotated genes (The 30 region contains 1,000 bases upstream of the 30 end and 100 bases downstream). UMI counting was done after marking duplicates (in-house script) using HTSeq-count in union mode. Only reads with unique mapping were considered for further analysis, and genes having minimum 5 reads in at least one sample were considered. Gene expression levels were calculated and normalized using DESeq2 with the parameters: betaPrior=True, cooksCutoff=FALSE, independentFilter- ing=FALSE. Batch correction was done using the sva (3.26.0) R when batch adjustments were required. Raw p-values were adjusted for multiple testing, using the procedure of Benjamini and Hochberg. Differentially expressed genes were selected with absolute fold change (log2)>1, and adjusted p-value <0.05. Visualization of gene expression heatmaps was done using Gene-e, using log normalized values. Clustering was applied on log2 transformed and standardized expression values, using the k-means algorithm (Euclidian method). For Gene Ontology (GO) term analysis, Metascape was used 57, and all heatmaps were made by Morpheus, https://software.broadinstitute.org/morpheus.
Assembly: mm10, Gencode annotation version 10.0
Supplementary files format and content: txt files, raw counts

molecule: polyA RNA

source_name: lung

extract_protocol: Peripheral blood or lung cells were isolated as previously described and sorted into 30 ul of lysis/binding buffer (home-made or Life Technologies) and stored at -80°C. mRNA was then captured with Dynabeads oligo(dT) (Life Technologies) according to the manufacturer’s guidelines. A bulk variation of MARSseq 77 was used for preparation of RNAseq libraries. Briefly, RNA was first reverse-transcribed with MARSseq barcoded RT primers with the Affinity Script kit (Agilent). Reverse transcription was analyzed by qRT-PCR and samples with a similar CT were pooled. Each pool was treated with Exonuclease I (NEB) for 30’ at 37°C. Double-stranded DNA was generated with the NEB second strand synthesis kit at 16°C for 2h.), Subsequently, in vitro transcription was performed over-night with the T7 High Yield RNA polymerase IVT kit (NEB) for 37°C overnight. Following IVT, the DNA template was removed with Turbo DNase I (Ambion) at 37°C for 15’. Amplified RNA was fragmented by incubation at 70°C for 3’ in Zn2+ RNA fragmentation reagent (Ambion). RNA was then ligated to the MARSseq ligation adaptor with T4 RNA Ligase I (NEB) at 22°C for 2h. Ligated product was reverse-transcribed using the Affinity Script RT enzyme (Agilent) and a primer complementary to the ligated product. The library was completed and amplified through a nested PCR reaction with P5_Rd1 and P7_Rd2 primers and PCR ready mix (Kappa Biosystems). Library concentrations was measured with a Qubit fluorometer (Life Technologies) and mean molecule size was determined with a 2200 TapeStation instrument. RNAseq libraries were sequenced using the Illumina NextSeq 500.

value: lung

tag: strain background

value: MDP-derived lung macrophage


title: NC3


title: NC1


title: SET-2, WT, DMSO, LSD1, Rep2


title: THP1_BRQ48_rep1_ATACseq

description: ATACseq


title: MCF7 shSMYD2 +DOX +Alpelisib rep 3

city: Baltimore

first: Eneda

last: Toska

state: MD

address: 1650 Orleans Street, CRB1

institute: Johns Hopkins University

data_processing:
salmon, v1.2.0
Assembly: hg18
Supplementary files format and content: .sf file including the transcript quantification results

growth_protocol: MCF7 cells were maintained in DMEM/F12 supplemented with 10% FBS and 1% penicillin streptomycin

extract_protocol:
Qiagen RNeasy Mini Kit
Illumina

treatment_protocol: Cells were cultured with dmso or 1ug/mL doxycycline for three days before starting the experiment. For the experiment cells were seeded and then treated 24 hours later with either DMSO or 1µM alpelisib. Cells were collected after 24 hours of drug treatment.

value: breast cancer

value: shSMYD2 +DOX +Alpelisib


title: THP1_BRQ24_rep2_ATACseq

description: ATACseq


title: SET-2, WT, DMSO, LSD1, Rep1


title: YAP-S127A3


title: THP1_HU_48h_rep1

description:
RNAseq
thp1_thp1_hu_100uM_48_1

data_processing:
Mouse and human data were mapped to mm10 and hg38 genomes, respectively, using STAR v2.7.8a and default parameters.
Reads that mapped to transcripts were counted using featureCounts v2.0.1 (with parameters -M -O --fraction --primary).
Genome_build: mm10
Genome_build: hg38
Supplementary_files_format_and_content: A tab-delimited file containing raw counts generated from featureCounts.

extract_protocol:
1 million live cells were sorted using a BD FACSAria and placed on ice. Immediately following the sort, cells were centrifuged, pelleted, and flash frozen in liquid nitrogen and placed at -80C. Pellets were processed in groups of 24 using the Zymo RNA Miniprep Kit and quantified using the Invitrogen Quant-it RNA kit. RNA was then diluted to a concentration of 2 ng/ul and 5ul of each sample was transferred to a 96 well plate.
Poly-A enrichment and cDNA synthesis were performed in parallel as described in Soumilion et al. 2014, followed by library preparation using the Nextera XT kit and paired-end sequencing on an Illumina NextSeq 500.

value: Hydroxyurea 100uM


title: SET-2, WT, GSK-LSD1, Input


title: MIM2


title: THP1_DMSO_rep2_ATACseq

description: ATACseq

value: DMSO 0.05percent


title: MCF7 shSMYD2  +DOX -Alpelisib rep 3

value: shSMYD2  +DOX -Alpelisib


title: MIM3


title: MCF7 shSMYD2 -DOX -Alpelisib rep 3

value: shSMYD2 -DOX -Alpelisib


title: THP1_BRQ24_rep1_ATACseq

description: ATACseq


title: SET-2, WT, GSKLSD1, GFI1B, Rep1

value: acute myeloid leukemia

value: WT


title: MCF7 shSMYD2 -DOX +Alpelisib rep 3

value: shSMYD2 -DOX +Alpelisib


title: SET-2, WT, DMSO, Input

value: Vehicle


title: MIM1


title: THP1_DMSO_rep1_ATACseq

description: ATACseq


title: iPS253-RPE, 6 weeks, rep1, cell4

value: iPSC derived RPE cell

value: RPE

value: 6 weeks


title: GIM4

value: GMP-derived lung macrophage


title: K562_sgNTC-1_BRQ250nM_72_rep3

data_processing:
Mouse and human data were mapped to mm10 and hg38 genomes, respectively, using STAR v2.7.8a and default parameters.
Reads that mapped to transcripts were counted using featureCounts v2.0.1 (with parameters -M -O --fraction --primary).
Supplementary files format and content: A tab-delimited file containing raw counts generated from featureCounts.

source_name: K562 dCas9-KRAB human CML cells (sgNTC-1)

extract_protocol:
1 million live cells were sorted using a BD FACSAria and placed on ice. Immediately following the sort, cells were centrifuged, pelleted, and flash frozen in liquid nitrogen and placed at -80C. Pellets were processed in groups of 24 using the Zymo RNA Miniprep Kit and quantified using the Invitrogen Quant-it RNA kit. RNA was then diluted to a concentration of 10 ng/ul and 10 ul of each sample was transferred to a 96 well plate.
Poly-A enrichment and library construction were performed using the NEB Ultra II RNAseq kit, and paired-end sequencing was performed on an Illumina NovaSeq S4.

value: Brequinar 250nM

tag: treatment duration

tag: genome build


title: MCF7 shSMYD2 +DOX +Alpelisib rep 2


title: THP_DMSO_IgG

description: CUT&RUN

data_processing:
Library strategy: CUT&RUN
Mouse and human data were mapped to mm10 and hg38 genomes, respectively, using Bowtie2 v2.4.2 (with parameters --dovetail -I 10 -X 700 --very-sensitive-local --local)
BAM files were then normalized to 10 million total reads.
Genome_build: mm10
Genome_build: hg38
Supplementary_files_format_and_content: Bigwig files for each sample

extract_protocol:
Cells were stained with a final concentration of 1 ng/ml DAPI in growth media, and 1 million live cells were sorted using a BD FACSAria and placed on ice. CUT&RUN was then performed using the Epicypher CUTANA CUT&RUN kit, using the indicated number of cells, antibody, and concentration of antibody.
Library construction was performed using the NEBNext Ultra II Library Preparation Kit following the indicated protocol, and each library was indexed using NEBNext® Multiplex Oligos for Illumina. For PU.1, the library construction protocol was modified to generate shorter fragments per https://www.protocols.io/view/library-prep-for-cut-amp-run-with-nebnext-ultra-ii-wvgfe3w. Libraries were quantified using Qubit and Bioanalyzer and pooled for sequencing using an Illumina NextSeq 500.

tag: antibody

value: IgG, Epicypher 13-0042

tag: cell number

tag: antibody concentration


title: K562_sgNTC-1_BRQ250nM_72_rep2


title: MCF7 shSMYD2  +DOX -Alpelisib rep 2


title: GIM3

value: lung


title: THP_PMA_48h_H3K27ac

description: CUT&RUN

value: PMA 100nM

value: H3K27ac, Millipore MABE647


title: MCF7 shSMYD2  -DOX +Alpelisib rep 2

value: breast cancer

value: shSMYD2  -DOX +Alpelisib


title: K562_sgNTC-1_BRQ250nM_72_rep1


title: THP_PMA_24h_H3K27ac

description: CUT&RUN


title: K562_sgNTC-1_DMSO_72_rep3


title: GIM1


title: MCF7 shSMYD2  -DOX -Alpelisib rep 2

value: shSMYD2  -DOX -Alpelisib


title: Bone marrow cells, ADT

description:
ADT: read1 contains cell barcode and UMI; read2 contains Antibody Derived Tag sequences
mouse_BM_ISC029_raw_feature_bc_matrix.h5
adt_feature_reference.csv
Metadata_Full_dataset_mouse_BM.csv
Metadata_Monocyte.DC.precursor.subset_mouse_BM.csv

library_source: other

data_processing:
Raw data bcl files were demultiplexed using Cellranger mkfastq
Demultiplexed data was processed using the Cellranger count pipeline
Assembly: mm10
Supplementary files format and content: Compressed .tar.gz files containing raw UMI counts in Cellranger output format, details for the ADT antibodies, and comma-delimited text files including metadata per cell

molecule: protein

source_name: Bone marrow

extract_protocol: All methods listed in Trzebanski et al. Murine classical monocyte subsets display differential functions and fates. Immunity. 2024

value: Bone marrow

tag: strain

tag: Sex

value: female

tag: age

value: 10 week-old

tag: library type

value: ADT


title: MCF7 shSMYD2  +DOX +Alpelisib rep 1

tag: cell line

value: shSMYD2  +DOX +Alpelisib


title: THP_BRQ_48h_H3K27ac

description: CUT&RUN

value: Brequinar 500nM


title: K562_sgNTC-1_DMSO_72_rep2


title: K562_sgNTC-1_DMSO_72_rep1


title: THP_BRQ_24h_H3K27ac

description: CUT&RUN


title: GIM2

tag: tissue

tag: cell type


title: Bone marrow cells, GEX

description:
3’ mRNA (v3.1 10x Genomics): read1 contains cell barcode and UMI; read2 contains transcript sequence
mouse_BM_ISC029_raw_feature_bc_matrix.h5
adt_feature_reference.csv
Metadata_Full_dataset_mouse_BM.csv
Metadata_Monocyte.DC.precursor.subset_mouse_BM.csv

library_source: transcriptomic single cell

value: mRNA


title: K562_sgBCR-1_NA_NA_rep3

source_name: K562 dCas9-KRAB human CML cells (sgBCR-1)


title: THP_PMA_48h_PU1

description: CUT&RUN


title: THP_DMSO_H3K27ac

description: CUT&RUN

value: DMSO 0.05percent


title: K562_sgBCR-1_NA_NA_rep2


title: MCF7 shSMYD2 -DOX -Alpelisib rep 1

value: shSMYD2 -DOX -Alpelisib


title: senescent mice

city: guangzhou

first: shanzhi

last: yang

address: 2nd zhongshan road

institute: guangdong provincial people's hospital

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: assembly mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus

source_name: kidney

extract_protocol:
Tissues were washed three times with PBS, cut into blocks of 2 mm and placed on DMEM-1640 medium (Gibco, Gaithersburg MD, USA).  Using buffer containing collagenase IV (1 mg/ml; Thermo Fisher), pronase E (1 mg/ml), and DNase I (50 U/ml), the tissues were digested at 37°C for 30 min.  Cells were filtered through a 70um cell strainer and centrifuged at 400×g for 5 minutes.  Take a small amount of single-cell suspension, add 0.4% trypan blue staining solution of the same volume, count the cells with Countess II Automated Cell Counter, and adjust the concentration of living cells to the ideal range (1000 to 2000 cells/μl).
The gel beads containing barcode information combine with a mixture of cells and enzymes,then enter the reservoir to be separated by oil to form GEMs (GelBeads-In-Emulsions).  After that, the gel beads dissolved and released the capture sequence containing the Barcode sequence, reverse transcribed the cDNA fragment, and labeled the sample.  Break up the gel beads and oil droplets then use cDNA as a template for PCR amplification.  All the products of GEMs are mixed to construct a standard sequencing library.  The cDNA was cut into 200~300bp fragments, then the second-generation sequencing library was constructed.  Finally, the DNA library was amplified by PCR.  The high-throughput sequencing of the library was carried out by using the PE150 sequencing mode of the Illumina sequencing platform.  Quality control of sequencing was performed using cellranger.

value: kidney


title: K562_sgNTC-1_NA_NA_rep3


title: MCF7 shSMYD2 -DOX +Alpelisib rep 1

value: shSMYD2 -DOX +Alpelisib


title: MCF7 shSMYD2  +DOX -Alpelisib rep 1

value: shSMYD2  +DOX -Alpelisib


title: THP_PMA_24h_PU1

description: CUT&RUN

value: PMA 100nM


title: THP_BRQ_48h_PU1

description: CUT&RUN


title: K562_sgNTC-1_NA_NA_rep1


title: THP_BRQ_24h_PU1

description: CUT&RUN


title: K562_sgNTC-1_NA_NA_rep2


title: lens clouded eyeball

city: Changchun

first: Shengnan

last: Han

state: Jilin

address: Xi'an road No.5333

institute: Jilin University

data_processing:
Quality assessment of sequenced raw data by FastQC v 0.11.2,Mass shearing by Trimmomatic to obtain relatively accurate and valid data
Mixing and splicing of sample valid data using Trinity
NCBI Blast+ was used to compare the transcripts with several databases such as CDD, KOG, COG, NR, NT and PFAM to obtain to obtain their functional annotation information.  KAAS was used to obtain KEGG annotation information of transcripts. CDS prediction was performed using TransDecoder.
The valid data of the samples were matched to the spliced transcripts using Bowtie2, and the Mapping information was counted.
SSR analysis was performed using MISA based on the sequence information of the transcripts obtained by splicing. The expression of genes was calculated using Salmon. Gene co-expression analysis was performed using WGCNA. Multi-directional statistical analysis and exploration such as sample comparison analysis based on the expression matrix of the samples. Gene expression differential analysis using DESeq2 to visualize the results of expression differential analysis. Based on the results of differential analysis, Venn diagram and heat map were drawn and cluster analysis was performed. Perform GO enrichment analysis using topGO and plot the significant GO directed acyclic graph. KEGG pathway and KOG classification enrichment analysis was performed using clusterProfiler.
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Myodes rufocanus

source_name: eyeball

extract_protocol:
RNA was harvested using Qubit RNA HS test kit. 1ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Hieff NGS™ MaxUp Dual-mode mRNA Library Prep Kit for  Illumina® following manufacturer's protocols.

value: eyeball


title: K562_sgBCR-1_NA_NA_rep1


title: normal eyeball


title: young mice


title: E-cig F 6% 3

status: Public on May 03 2024

type: RNA

city: Bloomington

first: Patricia

last: Silveyra

email: psilveyr@iu.edu, ptrcslvr@gmail.com

state: Indiana

department: Environmental and Occupational Health

institute: Indiana University Bloomington

description: female mouse exposed to vape (50%VG/50%PG) with 6% nitcotine

data_processing: Data were analyzed in excel using Ct values for each sample, normalized to the average Ct of 5 endogenous controls (Actb, B2m, Gapdh, Gusb, Hsp90ab1)

label: SYBR Green

source_name: lung tissue homogenate

label_protocol: A total of 100 ng of purified RNA were retrotranscribed with the RT2 First Strand Kit (Qiagen). The expression of 84 NRs genes and coregulators was measured with the RT² ProfilerTM Array Mouse Receptors & Coregulators (PAMM-056YE)

extract_protocol: Lung tissue was homogenized in Trizol. Total RNA was extracted with the Direct-zol (Zymo Research)

treatment_protocol: Adult male and female C57BL/6J mice were exposed to electronic cigarettes with 0%, 3% and 6% nicotine daily (70 ml, 3.3s, 1 puff per min/30 min) for 14 days, using the inExpose full body chamber (SCIREQ). Following exposure, lung tissue was harvested and RNA extracted.

tag: e-liquid exposure

value: yes

tag: nicotine %


title: E-cig F 6% 1


title: si-PGRN, biological rep2

city: Weifang

first: Panpan

last: Li

address: No.7166 Baotong West Street

institute: Shandong Second Medical University

description: Gene expression data from Human gastric cancer cells (BGC‐823)

hyb_protocol: Following fragmentation, 10ug of cRNA were hybridized for 16 hr at 45C on PrimeView Human Gene Expression Array. GeneChips were washed and stained in the GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 3000 .

data_processing: The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method.

label: biotin

source_name: Human gastric cancer cells (BGC-823)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 12ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

extract_protocol: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop 2000.

value: Human gastric cancer cells (BGC-823)

tag: treatment

value: si-PGRN


title: E-cig F 3% 2

description: female mouse exposed to vape (50%VG/50%PG) with 3% nitcotine


title: E-cig F 3% 4


title: E-cig F 6% 2


title: siNC , biological rep3

value: siNC


title: si-PGRN, biological rep1


title: siNC , biological rep2


title: E-cig F 0% 3

description: female mouse exposed to vape (50%VG/50%PG) with 0% nitcotine

value: female


title: E-cig F 3% 1


title: si-PGRN, biological rep3


title: siNC, biological rep1


title: E-cig M 6% 3

description: male mouse exposed to vape (50%VG/50%PG) with 6% nitcotine

value: male


title: No treatment F 3

description: female mouse not exposed (control)

value: no


title: E-cig F 3% 3


title: No treatment F 2

description: female mouse not exposed (control)


title: E-cig F 0% 1


title: E-cig F 0% 2


title: E-cig M 6% 2


title: THP_DMSO_PU1

description: CUT&RUN

tag: time point


title: E-cig M 6% 1


title: No treatment F 1

description: female mouse not exposed (control)


title: E-cig M 3% 4

description: male mouse exposed to vape (50%VG/50%PG) with 3% nitcotine


title: E-cig M 3% 1


title: V3

city: Beijing

first: Jiashu

last: Guo

address: No. 12, Zhongguancun South Street, Haidian District, Beijing

institute: Chinese Academy Of Agricultural Sciences

data_processing:
The clustering of the index-coded samples was performed on a cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia) according to the manufacturer’s instructions.
After cluster generation, the library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated.
Assembly: arsef_549
Supplementary files format and content: tab-delimited text file includes raw counts for each Sampletab-delimited text files include RPkM walues for each Sample

organism: Metarhizium anisopliae

source_name: ascomycete fungi

extract_protocol:
Total RNA was extract and RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA)
the library fragments were purified with AMPure XP system (Beckman Coulter, Beverly, USA). Then PCR amplification, the PCR product was purified by AMPure XP beads, and the library was finally obtained

value: hyphae

value: M.  anisopliae

tag: time

tag: genotype

value: virus-infected

value: cultured in cicada slough induced PBD medium


title: V1


title: E-cig M 0% 1

description: male mouse exposed to vape (50%VG/50%PG) with 0% nitcotine


title: E-cig M 3% 2


title: No treatment M 3

description: male mouse not exposed (control)


title: No treatment M 1

description: male mouse not exposed (control)


title: V2


title: E-cig M 0% 3


title: E-cig M 0% 2


title: F3

value: WT


title: F1


title: No treatment M 2

description: male mouse not exposed (control)


title: F2


title: E-cig M 3% 3


title: Lung, dzho rep3, scRNAseq

city: Chengdu

first: Daoliang

last: Lan

state: Sichuan

address: #16, South Section, 1st Ring Road

institute: Southwest Minzu University

description: 10× Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v5.0.0.
Assembly: ARS-UCD1.2
Supplementary files format and content: Tab-separated values files and matrix files.

organism: Bos grunniens x Bos taurus

extract_protocol:
Following aseptic procedures, for each individual, lung tissue samples of 1 cm³ in size were precisely collected using surgical scissors from 6 sampling points on both sides of the lung lobes (i.e. left anterior, left middle, left posterior, right anterior, right middle and right posterior lobes), located 5 cm from the lung apex, avoiding bronchial tubes and blood vessels as much as possible. Immediately, each piece of lung tissue was transferred separately to a freezing tube containing cell freezing medium (90% FBS and 10% DMSO) and thoroughly resuspended. For each animal, lung tissue samples collected from 6 different sites were pooled for subsequent single-cell transcriptomic analysis. Lung tissues in cryovials were thawed in a 37 °C water bath and washed 3 times in RPMI 1640 medium. The lung tissues were finely minced into approximately 0.5 mm³ fragments by using sterile surgical scissors in RPMI 1640 medium. These fragments were digested at 37 °C for 30 min in 1 mg/mL Type I collagenase, followed by 10 min of digestion at 37 °C in 0.25% trypsin-EDTA. Lastly, 10% foetal bovine serum was added to stop digestion. Lung tissue suspensions were filtered through a 40 μm cell strainer, and erythrocytes were removed with red blood cell lysis buffer. Lung cells were resuspended in DPBS containing 2% foetal bovine serum, and the cell suspension was counted and stored for subsequent scRNA-seq.
Library was performed according to the manufacter's instructions (single cell 3' v3 protocol, 10× Genomics). In brief, the whole library construction process was divided into 3 steps: GEM Generation & Barcoding, Post GEM-RT Cleanup & cDNA Amplification and 3' Gene Expression Library Construction.

value: lung


title: Lung, dzho rep1, scRNAseq

description: 10× Genomics


title: Lung, dzho rep2, scRNAseq

description: 10× Genomics


title: Vehicle_A6

city: Vienna

first: Daniel

last: Gerlach

address: Dr.-Boehringer-Gasse 5-11

department: Global Computational Biology and Digital Sciences

country: Austria

institute: Boehringer Ingelheim RCV GmbH & Co KG

data_processing:
*library strategy: Tru-seq
Multiplexed samples were sequenced on an Illumina NextSeq 2000 system. Base-calling was performed using the Real-Time Analysis (RTA) software version 2.4.11. Conversion of the raw bcl2 output files to gzipped FASTQ files was performed using the bcl2fastq2 software version 2.20.0 provided by Illumina.
Data was processed with a pipeline building upon the implementation of the ENCODE "Long RNA-seq" pipeline: In brief, single-end sequencing reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (source 1000 Genomes Project - GRCh38_full_analysis_set_plus_decoy_hla.fa,  excluding alternate contigs, chromosome mapping via grch38_ucsc2ensembl.txt) using the STAR (v2.5.2b) aligner allowing for soft clipping of adapter sequences. For quantification, transcript annotation files from Ensembl version 86 were used. Samples were quantified with the above annotations using featureCount (v1.5.1). Quality controls were implemented using FastQC (v0.11.5), picardmetrics (v0.2.4), and dupRadar (v1.0.0) at the respective steps. Finally, differential expression analysis was performed on the counts derived from featureCount using DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw featureCounts values for each Sample

source_name: lung carcinoma

growth_protocol: The cell lines were grown in the media recommended by the vendor and xenografted into mice.

extract_protocol:
Cells were lysed in TRI lysis reagent (Qiagen, #79306) according to the manufacturer's instructions. Total RNA was isolated with RNAeasy Mini Kit (Qiagen, #73404).
Tru-seq libraries were prepares using theTru-seq RNA Library Prep Kit v2 for Illumina from Lexogene (#015.96) according to manufacturer's instructions.

treatment_protocol: All mice had been treated with Adagrasib previously for 15 days before re-randomizing into 2 new groups: Group A = 8 mice were treated with Adagrasib continuously for 35 further days and Group B = 7 mice were treated with Adagrasib+SOS1i BI-3406 for 35 days. Adagrasib dose = 100 mg/kg qd, SOS1i BI-3406 = 50 mg/kg, bid.

value: lung carcinoma

value: lymphoblast

value: Vehicle


title: Vehicle_A5


title: Vehicle_A7


title: Vehicle_A2


title: Adagrasib_100mpk_BI3406_50mpk_B12


title: Adagrasib_100mpk_BI3406_50mpk_B14


title: Adagrasib_100mpk_BI3406_50mpk_B9


title: Adagrasib_100mpk_BI3406_50mpk_B15


title: Adagrasib_100mpk_A7


title: Vehicle_A3


title: Adagrasib_100mpk_A5


title: Adagrasib_100mpk_BI3406_50mpk_B13


title: Adagrasib_100mpk_BI3406_50mpk_B11


title: Adagrasib_100mpk_A4


title: Adagrasib_100mpk_A8


title: U2932_NOTCH2_Q2140_H3K27ac

city: Philadelphia

first: Luca

last: Busino

state: PA

address: 421 Curie Blvd, 705 BRB II/III

department: Cancer Biology

institute: Luca Busino

data_processing:
FASTQ files were aligned with BOWTIE2, reads were sorted and duplicate removed with SAMTOOLS.
Peaks were called with macs2.
Further analysis was performed in R-studio using the R packages Rsamtools, DEseq2, GenomicAlignments, soGGi, ggplot2, profileplyr.
Assembly: hg19
Supplementary files format and content: BigWig

source_name: lymphoid

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a S220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using NEBNext Ultra II DNA library prep with sample purification beads (NEB, E7103S) following the manufacturer's instruction. Libraries were amplified using 15 cycles on the thermocycler.

value: lymphoid

value: B-cell lymphoma

tag: chip antibody

value: H3K27ac (Abcam, ab4729)


title: U2932_NOTCH2_WT_Input


title: Adagrasib_100mpk_A6


title: Adagrasib_100mpk_A3


title: Vehicle_A4


title: U2932_NOTCH2_Q2140_RBP-J

value: RBP-J (Abcam, ab25949)


title: U2932_NOTCH2_WT_H3K27ac


title: Adagrasib_100mpk_A2


title: U2932_NOTCH2_WT_RBP-J


title: Vehicle_A1


title: U2932_NOTCH2_R2400_RBP-J


title: Adagrasib_100mpk_BI3406_50mpk_B10


title: LC_AD04

city: Amsterdam

first: Nina

last: van Sorge

address: Meibergdreef 9

country: Netherlands

institute: Amsterdam UMC

description:
wells O12-P20 are AD03 LCs, except for wells O21-O24 these contain spike-ins (barcodes: UMC-WM-s001_CCGAGATT-1, UMC-WM-s001_CTCTGCTA-1, UMC-WM-s001_TAGTTGCG-1, UMC-WM-s001_AGGCTAAC-1) same for wells P21-P24 (barcodes:UMC-WM-s001_CACCTCTA-1, UMC-WM-s001_AGTTGGAC-1, UMC-UMC-WM-s001_CTCTGTCT-1, WM-s001
UMC-WM-s015_H3CM5BGXM_S11

data_processing:
Read counts were UMI corrected to produce barcode counts
Supplementary files format and content: .tsv gene read counts (ReadCount) and UMI corrected read countd (BarcodeCounts)

source_name: epidermis

extract_protocol:
3mm biopsies were taken from atopic dermatitis patients (n=4) and healthy controls (n=3), Epidermis and dermis were separated after ON incubation and processed using the Miltenyi Epidermis Dissociation Kit or the Miltenyi Whol Skin Dissociation Kit, respectively. Single cell suspensions were stained and live LCs and T cells were sorted into 384-well plates containing vapor-lock (Qiagen) with 100-200 nl of primers, dNTPs and synthetic mRNA SpikeIns and were immediately centrifuged (2,000 x g) and frozen at -80⁰C
Illumina sequencing libraries were prepared with the TruSeq small RNA primers (Illumina) and sequenced single end at 75-bp read length with 75,000 reads per cell on a NextSeq500 platform (Illumina).
Sequencing reads were mapped against the reference human genome (GRCh38) using Burrows-Wheeler Alignment tool to create read counts

value: epidermis

tag: ID

value: langerhans cells

tag: disease state

value: atopic dermatitis


title: LC_AD01

description:
wells M14-P20 contain non lesional LCs from AD01, we excluded these from analysis. Except for wells O21-O24 , these contain spike-ins (barcodes: UMC-WM-s001_CCGAGATT-1, UMC-WM-s001_CTCTGCTA-1, UMC-WM-s001_TAGTTGCG-1, UMC-WM-s001_AGGCTAAC-1) same for wells P21-P24 (barcodes:UMC-WM-s001_CACCTCTA-1, UMC-WM-s001_AGTTGGAC-1, UMC-UMC-WM-s001_CTCTGTCT-1, WM-s001
UMC-WM-s014_H3GLJBGXM_S2


title: Tcell_HC02

description:
wells O21-O24 contain spike-ins (barcodes: UMC-WM-s001_CCGAGATT-1, UMC-WM-s001_CTCTGCTA-1, UMC-WM-s001_TAGTTGCG-1, UMC-WM-s001_AGGCTAAC-1) same for wells P21-P24 (barcodes:UMC-WM-s001_CACCTCTA-1, UMC-WM-s001_AGTTGGAC-1, UMC-UMC-WM-s001_CTCTGTCT-1, WM-s001
UMC-WM-s012_H3CM5BGXM_S10

source_name: dermis

value: dermis

value: T cells

value: healthy


title: Adagrasib_100mpk_A1


title: Tcell_AD01

description:
wells O21-O24 contain spike-ins (barcodes: UMC-WM-s001_CCGAGATT-1, UMC-WM-s001_CTCTGCTA-1, UMC-WM-s001_TAGTTGCG-1, UMC-WM-s001_AGGCTAAC-1) same for wells P21-P24 (barcodes:UMC-WM-s001_CACCTCTA-1, UMC-WM-s001_AGTTGGAC-1, UMC-UMC-WM-s001_CTCTGTCT-1, WM-s001
UMC-WM-s013_H3GLJBGXM_S1


title: Tcell_AD02

description:
wells O21-O24 contain spike-ins (barcodes: UMC-WM-s001_CCGAGATT-1, UMC-WM-s001_CTCTGCTA-1, UMC-WM-s001_TAGTTGCG-1, UMC-WM-s001_AGGCTAAC-1) same for wells P21-P24 (barcodes:UMC-WM-s001_CACCTCTA-1, UMC-WM-s001_AGTTGGAC-1, UMC-UMC-WM-s001_CTCTGTCT-1, WM-s001
UMC-WM-s010_H3CM5BGXM_S8


title: LC_AD02

description:
wells L1-L5, M1-P24 are empty, except for wells O21-O24, these contain spike-ins (barcodes: UMC-WM-s001_CCGAGATT-1, UMC-WM-s001_CTCTGCTA-1, UMC-WM-s001_TAGTTGCG-1, UMC-WM-s001_AGGCTAAC-1) same for wells P21-P24 (barcodes:UMC-WM-s001_CACCTCTA-1, UMC-WM-s001_AGTTGGAC-1, UMC-UMC-WM-s001_CTCTGTCT-1, WM-s001
UMC-WM-s009_H3CM5BGXM_S7


title: Tcell_HC03

description:
wells O21-O24 contain spike-ins (barcodes: UMC-WM-s001_CCGAGATT-1, UMC-WM-s001_CTCTGCTA-1, UMC-WM-s001_TAGTTGCG-1, UMC-WM-s001_AGGCTAAC-1) same for wells P21-P24 (barcodes:UMC-WM-s001_CACCTCTA-1, UMC-WM-s001_AGTTGGAC-1, UMC-UMC-WM-s001_CTCTGTCT-1, WM-s001
UMC-WM-s011_H3CM5BGXM_S9


title: Tcell_AD03

description:
wells O21-O24 contain spike-ins (barcodes: UMC-WM-s001_CCGAGATT-1, UMC-WM-s001_CTCTGCTA-1, UMC-WM-s001_TAGTTGCG-1, UMC-WM-s001_AGGCTAAC-1) same for wells P21-P24 (barcodes:UMC-WM-s001_CACCTCTA-1, UMC-WM-s001_AGTTGGAC-1, UMC-UMC-WM-s001_CTCTGTCT-1, WM-s001
UMC-WM-s008_H3CM5BGXM_S6


title: Plasma,T1D,S110

city: Siena

first: Francesco

last: Dotta

state: Si

address: Viale Bracci 16

department: Department of Medicine, surgery and neuroscience

country: Italy

institute: University of Siena

data_processing:
Reads were aligned referring to miRbase v20 using HTG Parser software
Assembly: GRCh38/hg38
Supplementary files format and content: semicolon separated value file includes raw counts for each Sample

source_name: plasma

extract_protocol:
RNA extraction-free approach, and exploit quantitative nuclease protection assay (qNPA) chemistry
Concentration has been evaluated through HTG EdgeSeq KAPA Library quantification, and each library has been normalized and pooled using HTG EdgeSeq RUO library calculator

value: plasma


title: Plasma,T1D,S86


title: Plasma,T1D,S91


title: Plasma,T1D,S109


title: LC_AD03

description:
wells O21-O24 contain spike-ins (barcodes: UMC-WM-s001_CCGAGATT-1, UMC-WM-s001_CTCTGCTA-1, UMC-WM-s001_TAGTTGCG-1, UMC-WM-s001_AGGCTAAC-1) same for wells P21-P24 (barcodes:UMC-WM-s001_CACCTCTA-1, UMC-WM-s001_AGTTGGAC-1, UMC-UMC-WM-s001_CTCTGTCT-1, WM-s001
UMC-WM-s007_H3CM5BGXM_S5


title: LC_HC02

description:
wells O21-O24 contain spike-ins (barcodes: UMC-WM-s001_CCGAGATT-1, UMC-WM-s001_CTCTGCTA-1, UMC-WM-s001_TAGTTGCG-1, UMC-WM-s001_AGGCTAAC-1) same for wells P21-P24 (barcodes:UMC-WM-s001_CACCTCTA-1, UMC-WM-s001_AGTTGGAC-1, UMC-UMC-WM-s001_CTCTGTCT-1, WM-s001_AGTGCAGA-1)
UMC-WM-s001_H3CM5BGXM_S1


title: U2932_NOTCH2_R2400_H3K27ac


title: LC_HC03

description:
wells O21-O24 contain spike-ins (barcodes: UMC-WM-s001_CCGAGATT-1, UMC-WM-s001_CTCTGCTA-1, UMC-WM-s001_TAGTTGCG-1, UMC-WM-s001_AGGCTAAC-1) same for wells P21-P24 (barcodes:UMC-WM-s001_CACCTCTA-1, UMC-WM-s001_AGTTGGAC-1, UMC-UMC-WM-s001_CTCTGTCT-1, WM-s001_AGTGCAGA-1)
UMC-WM-s002_H3CM5BGXM_S2


title: Plasma,T1D,S20


title: Plasma,T1D,S21


title: Plasma,T1D,S83


title: Tcell_HC01

description:
wells O21-O24 contain spike-ins (barcodes: UMC-WM-s001_CCGAGATT-1, UMC-WM-s001_CTCTGCTA-1, UMC-WM-s001_TAGTTGCG-1, UMC-WM-s001_AGGCTAAC-1) same for wells P21-P24 (barcodes:UMC-WM-s001_CACCTCTA-1, UMC-WM-s001_AGTTGGAC-1, UMC-UMC-WM-s001_CTCTGTCT-1, WM-s001
UMC-WM-s004_H3CM5BGXM_S4


title: Plasma,T1D,S19


title: LC_HC01

description:
wells O21-O24 contain spike-ins (barcodes: UMC-WM-s001_CCGAGATT-1, UMC-WM-s001_CTCTGCTA-1, UMC-WM-s001_TAGTTGCG-1, UMC-WM-s001_AGGCTAAC-1) same for wells P21-P24 (barcodes:UMC-WM-s001_CACCTCTA-1, UMC-WM-s001_AGTTGGAC-1, UMC-UMC-WM-s001_CTCTGTCT-1, WM-s001
UMC-WM-s003_H3CM5BGXM_S3


title: Plasma,T1D,S81b


title: Plasma,T1D,S17


title: Plasma,T1D,S48


title: Plasma,T1D,S81


title: Plasma,T1D,S114


title: Plasma,T1D,S26


title: Plasma,T1D,S23


title: Plasma,T1D,S2


title: Plasma,T1D,S22


title: Plasma,T1D,S12


title: Plasma,T1D,S78


title: Plasma,T1D,S31


title: Plasma,T1D,S89


title: Plasma,T1D,S47


title: Plasma,T1D,S14


title: Plasma,T1D,S36


title: Plasma,T1D,S13


title: Plasma,T1D,S113


title: Plasma,T1D,S37


title: Plasma,T1D,S33


title: Plasma,T1D,S16


title: Plasma,T1D,S88


title: Plasma,T1D,S34


title: Plasma,T1D,S84


title: Plasma,T1D,S10


title: Plasma,T1D,S90


title: Plasma,T1D,S82b


title: Plasma,T1D,S15


title: Plasma,T1D,S72


title: Plasma,T1D,S73


title: Plasma,T1D,S106


title: Plasma,T1D,S79


title: Plasma,T1D,S71


title: Plasma,T1D,S27


title: Plasma,T1D,S87


title: Plasma,T1D,S74


title: Plasma,T1D,S43


title: Plasma,T1D,S70


title: Plasma,T1D,S8


title: Plasma,T1D,S69


title: Plasma,T1D,S42


title: Plasma,T1D,S7


title: Plasma,T1D,S106b


title: Plasma,T1D,S6


title: Plasma,T1D,S4


title: Plasma,T1D,S105


title: Plasma,T1D,S108


title: Plasma,T1D,S5


title: Plasma,T1D,S52


title: Plasma,T1D,S50


title: Plasma,T1D,S102


title: Plasma,T1D,S44


title: Plasma,T1D,S3


title: Plasma,T1D,S24


title: Plasma,T1D,S38


title: Plasma,T1D,S41


title: Plasma,T1D,S104


title: Plasma,T1D,S112


title: Plasma,T1D,S82


title: Plasma,T1D,S111


title: Plasma,T1D,S40


title: Plasma,T1D,S53


title: Plasma,T1D,S11


title: Plasma,T1D,S107


title: Plasma,T1D,S9


title: Plasma,T1D,S6b


title: Plasma,T1D,S29


title: Plasma,T1D,S92


title: Plasma,T1D,S51


title: Plasma,T1D,S95


title: Plasma,T1D,S93


title: Plasma,T1D,S97


title: Plasma,T1D,S94


title: Plasma,T1D,S101


title: Plasma,T1D,S45


title: Plasma,T1D,S96


title: Plasma,T1D,S28


title: Plasma,T1D,S77


title: Plasma,T1D,S103


title: Plasma,T1D,S75


title: Plasma,T1D,S18


title: Plasma,T1D,S66


title: Plasma,T1D,S39


title: Plasma,T1D,S46


title: Plasma,T1D,S35


title: Plasma,T1D,S76


title: Plasma,T1D,S63


title: Plasma,T1D,S64


title: Plasma,T1D,S65


title: Plasma,T1D,S85


title: Plasma,T1D,S100


title: Plasma,T1D,S60


title: Plasma,T1D,S61


title: Plasma,T1D,S30


title: Plasma,T1D,S80


title: Plasma,T1D,S1


title: Plasma,T1D,S49


title: Plasma,T1D,S68


title: Plasma,T1D,S54b


title: Plasma,T1D,S67


title: Plasma,T1D,S25


title: Plasma,T1D,S98


title: Plasma,T1D,S99


title: Plasma,T1D,S57


title: Plasma,T1D,S59


title: Plasma,T1D,S58


title: Plasma,T1D,S56


title: Plasma,T1D,S55


title: Plasma,T1D,S62


title: NCI-H2122 cells, Adagrasib_100mpk_TNO155_10mpk_48h_P65

data_processing:
Multiplexed samples were sequenced on an Illumina NextSeq 500 system. Base-calling was performed using the Real-Time Analysis (RTA) software version 2.4.11. Conversion of the raw bcl2 output files to gzipped FASTQ files was performed using the bcl2fastq2 software version 2.20.0 provided by Illumina.
Data was processed with a pipeline building upon the implementation of the ENCODE "Long RNA-seq" pipeline: In brief, single-end sequencing reads were mapped against the Homo sapiens (human) genome hg38/GRCh38 (source 1000 Genomes Project - GRCh38_full_analysis_set_plus_decoy_hla.fa,  excluding alternate contigs, chromosome mapping via grch38_ucsc2ensembl.txt) using the STAR (v2.5.2b) aligner allowing for soft clipping of adapter sequences. For quantification, transcript annotation files from Ensembl version 86 were used. Samples were quantified with the above annotations using featureCount (v1.5.1). Quality controls were implemented using FastQC (v0.11.5), picardmetrics (v0.2.4), and dupRadar (v1.0.0) at the respective steps. Finally, differential expression analysis was performed on the counts derived from featureCount using DESeq2
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include raw featureCounts values for each Sample

extract_protocol:
Cells were lysed in TRI lysis reagent (Qiagen, #79306) according to the manufacturer's instructions. Total RNA was isolated with RNAeasy Mini Kit (Qiagen, #73404).
Quant-seq libraries were prepares using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina from Lexogene (#015.96) according to manufacturer's instructions.
QUANT-seq


title: Plasma,T1D,S54


title: Plasma,T1D,S32


title: NCI-H2122 cells, Adagrasib_100mpk_TNO155_10mpk_24h_N57


title: NCI-H2122 cells, Adagrasib_100mpk_TNO155_10mpk_24h_N56


title: NCI-H2122 cells, Adagrasib_100mpk_TNO155_10mpk_48h_P64


title: NCI-H2122 cells, Adagrasib_100mpk_TNO155_10mpk_48h_P62


title: NCI-H2122 cells, Adagrasib_100mpk_TNO155_10mpk_24h_N55


title: NCI-H2122 cells, Adagrasib_100mpk_TNO155_10mpk_4h_O60


title: NCI-H2122 cells, BI3406_50mpk_Adagrasib_100mpk_48h_M52


title: NCI-H2122 cells, Adagrasib_100mpk_TNO155_10mpk_48h_P63


title: NCI-H2122 cells, Adagrasib_100mpk_TNO155_10mpk_4h_O61


title: NCI-H2122 cells, Adagrasib_100mpk_TNO155_10mpk_4h_O59


title: NCI-H2122 cells, BI3406_50mpk_Adagrasib_100mpk_48h_M51


title: NCI-H2122 cells, Adagrasib_100mpk_TNO155_10mpk_24h_N54


title: NCI-H2122 cells, BI3406_50mpk_Adagrasib_100mpk_48h_M53


title: NCI-H2122 cells, BI3406_50mpk_Adagrasib_100mpk_48h_M50


title: NCI-H2122 cells, BI3406_50mpk_Adagrasib_100mpk_24h_K45


title: NCI-H2122 cells, BI3406_50mpk_Adagrasib_100mpk_4h_L47


title: NCI-H2122 cells, BI3406_50mpk_Adagrasib_100mpk_4h_L49


title: NCI-H2122 cells, BI3406_50mpk_Adagrasib_100mpk_24h_K44


title: NCI-H2122 cells, BI3406_50mpk_Adagrasib_100mpk_4h_L48


title: NCI-H2122 cells, TNO155_10mpk_48h_J41


title: NCI-H2122 cells, BI3406_50mpk_Adagrasib_100mpk_4h_L46


title: NCI-H2122 cells, TNO155_10mpk_48h_J40


title: NCI-H2122 cells, TNO155_10mpk_48h_J38


title: NCI-H2122 cells, TNO155_10mpk_24h_H33


title: NCI-H2122 cells, TNO155_10mpk_24h_H30


title: NCI-H2122 cells, TNO155_10mpk_4h_I36


title: NCI-H2122 cells, BI3406_50mpk_Adagrasib_100mpk_24h_K42


title: NCI-H2122 cells, TNO155_10mpk_4h_I37


title: NCI-H2122 cells, Adagrasib_100mpk_TNO155_10mpk_4h_O58


title: NCI-H2122 cells, Adagrasib_100mpk_48h_G29


title: NCI-H2122 cells, TNO155_10mpk_24h_H32


title: NCI-H2122 cells, TNO155_10mpk_48h_J39


title: NCI-H2122 cells, TNO155_10mpk_4h_I35


title: NCI-H2122 cells, TNO155_10mpk_4h_I34


title: NCI-H2122 cells, Adagrasib_100mpk_48h_G27


title: NCI-H2122 cells, Adagrasib_100mpk_48h_G26


title: NCI-H2122 cells, Adagrasib_100mpk_48h_G28


title: NCI-H2122 cells, BI3406_50mpk_Adagrasib_100mpk_24h_K43


title: NCI-H2122 cells, Adagrasib_100mpk_24h_E21


title: NCI-H2122 cells, Adagrasib_100mpk_24h_E18


title: NCI-H2122 cells, Adagrasib_100mpk_24h_E20


title: NCI-H2122 cells, Adagrasib_100mpk_24h_E19


title: NCI-H2122 cells, Adagrasib_100mpk_4h_F24


title: NCI-H2122 cells, Adagrasib_100mpk_4h_F25


title: NCI-H2122 cells, Adagrasib_100mpk_4h_F23


title: NCI-H2122 cells, Adagrasib_100mpk_4h_F22


title: NCI-H2122 cells, BI3406_50mpk_48h_D17


title: NCI-H2122 cells, TNO155_10mpk_24h_H31


title: NCI-H2122 cells, BI3406_50mpk_48h_D15


title: NCI-H2122 cells, BI3406_50mpk_48h_D14


title: NCI-H2122 cells, BI3406_50mpk_24h_B9


title: NCI-H2122 cells, BI3406_50mpk_24h_B8


title: NCI-H2122 cells, BI3406_50mpk_24h_B7


title: NCI-H2122 cells, BI3406_50mpk_24h_B6


title: NCI-H2122 cells, Vehicle_A5


title: NCI-H2122 cells, BI3406_50mpk_4h_C11


title: NCI-H2122 cells, BI3406_50mpk_4h_C10


title: NCI-H2122 cells, Vehicle_A3


title: NCI-H2122 cells, Vehicle_A2


title: NCI-H2122 cells, Vehicle_A4


title: U2932_NOTCH2_Q2140_biol_rep_2

data_processing:
STAR to align
Samtools to sort and build index
Feature counts to quantify row counts
Deseq2 for differential expression analysis
Assembly: Genome is GRCh38
Supplementary files format and content: tab-delimited text files include normalized counts for each sample

extract_protocol:
Total RNA was extracted using Rneasy Mini Kit (Qiagen, 74104) and polyA+ transcripts were isolated with NEBNext Poly(A) mRNA magnetic isolation module (NEB, 7490)
RNA-seq libraries were prepared with NEBNext Ultra Directional RNA Library Prep Kit for Illumina (NEB, E7420)

value: xenotransplanted into NSG mice and treated with CHOP (cyclophosphamide, doxorubicin, vincristine, and prednisone), RNA-seq samples were collected when tumor volumes reach 1cm3


title: U2932_NOTCH2_R2400_biol_rep_3


title: U2932_NOTCH2_Q2140_biol_rep_1


title: NCI-H2122 cells, Vehicle_A1


title: U2932_NOTCH2_R2400_biol_rep_2


title: U2932_NOTCH2_R2400_biol_rep_1


title: U2932_NOTCH2_S2156A_biol_rep_3


title: U2932_NOTCH2_S2156A_biol_rep_2


title: U2932_NOTCH2_Q2140_biol_rep_3


title: U2932_NOTCH2_WT_biol_rep_3


title: NCI-H2122 cells, BI3406_50mpk_48h_D16


title: C3A-LX2 spheroids, TPN1%, 144h, rep2

city: Brussels

first: Milos

last: Mihajlovic

address: Laarbeeklaan 103

country: Belgium

institute: Vrije Universiteit Brussel

description: processed data FPKM in column K (fpkm_TPN_144h_n2) in the matrix core table

data_processing:
SOAPnuke software (v1.5.2; BGI Genomics) was used for filtering. The reads containing the adaptor (adaptor pollution), reads with with N content greater than 5% and low-quality reads (reads with bases with a quality score less than 15 as the proportion of total bases in the reads that are greater than 20%) were removed. The filtered "Clean Reads" were saved in FASTQ format. Parameters:  -l 15 -q 0.2 -n 0.05
The filtered clean reads were aligned to the reference human genome assembly GRCh38.p13 (version GCF_000001405.39_GRCh38.p13) using Bowtie2 software (v2.2.5) and HISAT2 (v2.0.4). Parameters：--sensitive --no-discordant --no-mixed -I 1 -X 1000 -p 8 --rna-strandness RF
Assembly: Homo_sapiens_NCBI_GCF_000001405.39_GRCh38.p13
Supplementary files format and content: excel table containing FPKM values for each Sample (xls file)

source_name: HepG2/C3A, LX-2

growth_protocol: HepG2/C3A and LX-2 cells were cultured in Minimum Essential Medium (MEM) supplemented with 1 mM sodium pyruvate, 1% non-essential amino acids, 10% fetal bovine serum, 100 U/ml penicillin, and 100 μg/ml streptomycin at 37 °C, at 5% CO2.

extract_protocol:
RNA was harvested using RNeasy Mini kit (Qiagen).
Strand-Specific Transcriptome Library Construction. Following mRNA purification from total RNA samples, mRNA was fragmented and used to synthesize first-strand cDNA, and then second-strand cDNA. After the end repair was performed, adapter sequences were ligated. After the PCR amplification step, the library was validated using Agilent Technologies 2100 bioanalyzer. Following this step, circularization was performed to obtain single-strand circle DNA which was formatted as the final library. The library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecule. The DNBs were then loaded into a patterned nanoarray and sequenced.

treatment_protocol: Human liver co-culture liver spheroids were exposed to 1% of total parenteral nutrition for 24h or 144h, using untreated cells as control.

value: HepG2/C3A, LX-2

value: hepatocytes and hepatic stellate cells co-culture

value: treatment with 1% total parenteral nutrition (TPN) for 144h


title: C3A-LX2 spheroids, untreated, 144h, rep3

description: processed data FPKM in column F (fpkm_Ctrl_144h_n3) in the matrix core table

value: no treatment


title: U2932_NOTCH2_S2156A_biol_rep_1


title: NCI-H2122 cells, BI3406_50mpk_4h_C12

value: lung carcinoma


title: C3A-LX2 spheroids, TPN1%, 144h, rep1

description: processed data FPKM in column J (fpkm_TPN_144h_n1) in the matrix core table


title: C3A-LX2 spheroids, TPN1%, 144h, rep3

description: processed data FPKM in column L (fpkm_TPN_144h_n3) in the matrix core table


title: U2932_NOTCH2_WT_biol_rep_2

value: lymphoid


title: C3A-LX2 spheroids, untreated, 144h, rep1

description: processed data FPKM in column D (fpkm_Ctrl_144h_n1) in the matrix core table


title: NCI-H2122 cells, BI3406_50mpk_4h_C13


title: U2932_DKO_biol_rep_2

value: B-cell lymphoma


title: U2932_DKO_biol_rep_3


title: C3A-LX2 spheroids, untreated, 144h, rep2

description: processed data FPKM in column E (fpkm_Ctrl_144h_n2) in the matrix core table


title: C3A-LX2 spheroids, TPN1%, 24h, rep3

description: processed data FPKM in column O (fpkm_TPN_24h_n3) in the matrix core table

value: treatment with 1% total parenteral nutrition (TPN) for 24h


title: U2932_N2_KO_biol_rep_3


title: U2932_DKO_biol_rep_1


title: C3A-LX2 spheroids, TPN1%, 24h, rep1

description: processed data FPKM in column M (fpkm_TPN_24h_n1) in the matrix core table


title: C3A-LX2 spheroids, TPN1%, 24h, rep2

description: processed data FPKM in column N (fpkm_TPN_24h_n2) in the matrix core table


title: C3A-LX2 spheroids, untreated, 24h, rep3

description: processed data FPKM in column I (fpkm_Ctrl_24h_n3) in the matrix core table


title: C3A-LX2 spheroids, untreated, 24h, rep2

description: processed data FPKM in column H (fpkm_Ctrl_24h_n2) in the matrix core table


title: C3A-LX2 spheroids, untreated, 24h, rep1

description: processed data FPKM in column G (fpkm_Ctrl_24h_n1) in the matrix core table


title: U2932_N2_KO_biol_rep_1


title: U2932_K6_KO_biol_rep_3


title: U2932_N2_KO_biol_rep_2


title: U2932_K6_KO_biol_rep_1


title: U2932_K6_KO_biol_rep_2


title: Soybean, +ORF1, +ORF2, +Cas9

city: St. Louis

first: R. Keith

last: Slotkin

state: Missouri

address: 975 North Warson Road

institute: Donald Danforth Plant Science Center

data_processing:
To identify and characterize reads that have both mPing and other regions of the genome, the 3’ adapter was trimmed from raw reads using cutadapt (parameters: -a "ATCACTAGTGAATTCGCGGCC;min_overlap=10;e=0.1" -q 10). Next, only reads containing mPing sequence were identified and the matching mPing sequence was trimmed from the 5’ end using cutadapt (parameters: -g "EXPECTEDMPINGSEQUENCE;min_overlap=35;e=0.1" -q 10).
To remove reads that show mPing at its donor location, these 5’ and 3’ trimmed sequences were mapped to the reference mPing donor sequence using default parameters of bowtie2 with the additional parameter to store donor-unmapped reads (--un). These donor-unmapped reads were then mapped to the genome using default parameters of bowtie2. The start position of each mapping read was collected as the mPing insertion site into the genome.
Assembly: TAIR10 for Arabidopsis and Williams 82 reference genome (Wm82.a4.v1) from Phytozome for soybean.
Supplementary files format and content: A tab-delimited file showing the start site of each read supporting a genomic insertion site is supplied as a processed file. The four columns are chromosome, start site, strand, and sequence of the read.
Library strategy: DNA-seq

organism: Glycine max

source_name: leaf

growth_protocol: Arabidopsis thaliana: All plants were grown at 22℃ under 16-hour day conditions in a MTPS-120 growth chamber with 200 µmol m−2 s−1 light intensity.    Glycine max: Plants are grown in the chamber under the following conditions. Temperature: 25°C day/ 23°C night (77°F/73°F); Humidity: 50%; Light: 14-hour day at 200-600 μmol. Regenerated transgenic plants were then transplanted into a greenhouse to mature with following conditions. Temperature: 25°C day/ 23°C night (77°F/73°F); Humidity: 35% minimum; Light: The supplemental lights come on when the sunlight is below 400 W/m²between 6am-8pm (14 hours) from September through May and between 6-10am May through September; Shading: The shade curtain automatically closes to 50% when the sunlight level is over 900 W/m² and it pulls to 100% when the sunlight is over 1000 W/m².

extract_protocol:
High molecular weight DNA was isolated from fresh Arabidopsis seedlings and Soybean leaf tissue using the NucleoBond HMW DNA kit (Takara), and digested by restriction enzymes XbaⅠ and AluⅠ.
Fragmented DNAs ranging from ~450bp to ~2kb were purified from agarose gels, A-tailed by Klenow Fragment (3’-5’ exo-; NEB), and ligated to the pGEM T- Easy vector (Promega). 1 µL of this ligation product was used as a template for primary PCR, followed by secondary PCR using nested primers. mPing specific primers were used with the pGEM T- Easy vector primers for primary and secondary PCRs.  Barcoded sequencing adapters were added to the amplicons through their inclusion in the PCR primers. The sequencing library for soybean was constructed similarly, except that the genomic DNA was isolated from leaf tissue and digested by XbaⅠ, PmlⅠ, and AluⅠ.
After passing quality controls, libraries were run on a MiSeq (Illumina) with V2 output (1X300)

treatment_protocol: Arabidopsis thaliana: Various binary vectors were introduced into Agrobacterium tumefaciens GV3101. All transgenic lines were transformed using the Agrobacterium-mediated floral dip method and subsequent selection for Hygromycin-resistant plants.    Glycine max: Various binary vectors were introduced into Agrobacterium tumefaciens AGL1. Mature half-seeds of Soybean (Glycine max var. Williams 82) were transformed to generate transgenic plants using a modified version of the method adapted from a previous publication (PMID: 25300848). Transgenic plants were selected for Basta-resistance and confirmed by PCR.

value: leaf

value: Wt + specific transgenes

tag: cultivar

value: Williams 82


title: BMDM, treated, 24 hours, rep3

city: Freiburg im Breisgau

first: Angelika

last: Rambold

address: Stübeweg 51

department: Department of Developmental Immunology

country: Germany

institute: Max Planck Institute of Immunobiology and Epigenetics

description:
batch2
BMDM_24h_rep3

data_processing:
snakePipes 2.7.2 was used to generate the count matrix
Supplementary files format and content: counts.tsv

source_name: BMDM

extract_protocol:
RNeasy MinElute Cleanup Kit
TruSeq Stranded mRNA protocol

value: BMDM

value: WT

value: LPS/IFNg


title: U2932_NOTCH2_WT_biol_rep_1


title: BMDM, treated, 24 hours, rep2

description:
batch2
BMDM_24h_rep2


title: BMDM, treated, 24 hours, rep1

description:
batch2
BMDM_24h_rep1


title: BMDM, treated, 6 hours, rep2

description:
batch1
BMDM_6h_rep2


title: U2932_KLHL6_KO_OP9_DLL1_12h_biol_rep_2


title: U2932_WT_biol_rep_1


title: BMDM, treated, 6 hours, rep1

description:
batch1
BMDM_6h_rep1


title: U2932_KLHL6_KO_OP9_DLL1_12h_biol_rep_3


title: BMDM, treated, 2 hours, rep2

description:
batch1
BMDM_2h_rep2


title: U2932_KLHL6_KO_OP9_DLL1_8h_biol_rep_2


title: BMDM, untreated, 0 hours, rep4

description:
batch2
BMDM_0h_rep4

value: untreated


title: U2932_KLHL6_KO_OP9_DLL1_8h_biol_rep_3


title: BMDM, treated, 2 hours, rep1

description:
batch1
BMDM_2h_rep1


title: U2932_KLHL6_KO_OP9_DLL1_8h_biol_rep_1


title: BMDM, untreated, 0 hours, rep5

description:
batch2
BMDM_0h_rep5


title: U2932_KLHL6_KO_OP9_DLL1_12h_biol_rep_1


title: U2932_KLHL6_KO_OP9_DLL1_3h_biol_rep_3


title: U2932_KLHL6_WT_OP9_DLL1_12h_biol_rep_3


title: BMDM, untreated, 0 hours, rep2

description:
batch1
BMDM_0h_rep2


title: U2932_KLHL6_WT_OP9_DLL1_12h_biol_rep_2


title: U2932_WT_biol_rep_3


title: U2932_WT_biol_rep_2


title: U2932_KLHL6_WT_OP9_DLL1_8h_biol_rep_3


title: U2932_KLHL6_KO_OP9_DLL1_3h_biol_rep_2


title: U2932_KLHL6_KO_OP9_DLL1_0h_biol_rep_3


title: U2932_KLHL6_KO_OP9_DLL1_0h_biol_rep_2


title: U2932_KLHL6_KO_OP9_DLL1_3h_biol_rep_1


title: U2932_KLHL6_WT_OP9_DLL1_3h_biol_rep_3


title: BMDM, untreated, 0 hours, rep1

description:
batch1
BMDM_0h_rep1


title: U2932_KLHL6_KO_OP9_DLL1_0h_biol_rep_1


title: U2932_KLHL6_WT_OP9_DLL1_0h_biol_rep_1


title: U2932_KLHL6_WT_OP9_DLL1_0h_biol_rep_2


title: U2932_KLHL6_WT_OP9_DLL1_0h_biol_rep_3


title: U2932_KLHL6_WT_OP9_DLL1_12h_biol_rep_1


title: iPSC 176/1 polCA6_medial

city: wien

first: Camilla

last: Bosone

state: Austria

address: Dr Bohr gasse 3

institute: IMBA

data_processing:
Basecalling: RTA 2.4.11
Adapter have been clipped with trimgalore (v0.5.0)
Abundant sequences (iGenomes hg38) are removed with bowtie2 (v2.3.4.1).
Cleaned reads are aligned against the genome (GRCh38) with STAR (v2.6.0c).
Reads are counted towards their corresponding gene (ENSEMBL v94) with featureCounts (v1.6.2).
Assembly: GRCh38
Supplementary files format and content: feature count output file (tab-separated; last column contains counts)

source_name: iPSC line reprogrammed at VBCF

growth_protocol: Organoids were generated with a modified version of what previously described (Lancaster and Knoblich, 2014; Lancaster et al., 2013). Briefly, on D0 hESCs and iPSCs  were treated with accutase to single cell suspention and transferred to an ultra-low binding 96-well plate (9000 cells/well) for rOrgs, or to a PMDS mould (5,5x106 cells/mould) for eOrgs. Cells aggregated into embrioyd bodies in mTeSR1 supplemented with 50 µM Rho-associated protein kinase (ROCK) inhibitor. PMDS moulds have been sterilized with autoclaving and gamma irradiation, then treated with Pluronic F127 (Sigma-Aldrich P2443) 1% in PBS and wash with PBS several times prior to usage. From D1 on, the medium was replaced daily with Neural Induction Medium (NI) containing DMEM-F12 supplemented with 1X N2 supplement, 1ug/ml heparin solution, 1X GlutaMAX, 1X MEM-NEAA and 50 µM ROCK inhibitor. On D7, embryoid bodies were embedded into droplets of Matrigel and transferred into 6-cm dishes containing Imp-A Medium consisting of 50% DMEM-F12, 50% Neurobasal medium, 1X N2, 1X B27 – Vitamin A, 2.5 g/ml Insulin, 0.05mM BME, 1X GlutaMAX, 1X MEM-NEAA and 1X Antibiotic-Antimycotic (Thermo Fisher 15240062). On D15, media was replaced with Imp+A Medium consisting of 50% DMEM-F12, 50% Neurobasal medium, 1X N2, 1X B27, 2.5 µg /ml Insulin, 0.05mM BME, 1X GlutaMAX, 1X MEM-NEAA, 1X Antibiotic-Antimycotic and organoids were moved to on an orbital shaker under 52 rpm rotating speed. The medium was changed every 2-3 days. From D30 onwards, organoids were fed with Imp+A Medium supplemented with 1% (v/v) matrigel basement membrane, BDNF (20 ng/ml) and GDNF (20 ng/ml)

extract_protocol:
All the polCAs and control (conCAs) have been manually dissected at a stereomicroscope and processed for RNA extraction. For bulk RNAseq, samples were lysed in 350 µl of RLT buffer supplemented with βmercaptoehtanol and RNA was extracted using the RNeasy Micro Kit (Qiagen 74004) following the manufacturer’s protocol. For scRNAseq, manually dissected at a stereomicroscope and processed for dissociation with gentleMACSTM Dissociator in Trypsin/Accutase solution with TURBO™ DNase (Thermo AM2238, 2 U/µL). After dissociation, DPBS-/- + 10% FBS has been gradually added to stop reaction. Samples have been then centrifuged at 400G for 5min at 4ºC and supernatant was aspirated without touching the pellet. The pellet has been resuspended in additional  500µl of DPBS-/- + 10% FBS, filtered through FACS tubes and stained for viability dye DRAQ7 (Biostatus, DR70250, 0.3mM). Live cells have been sorted with a BD FACS Aria™ III on Alexa 700 filter and barcoded with unique CMOs for MULTI-seq analysis.
For bulk RNAseq, we then assessed RNA concentration and quality with an RNA 6000 Nano Chip (Agilent Technologies) and enriched for mRNA with NEBNext Poly(A) mRNA Magnetic Isolation Module; barcoded samples were then multiplexed and sequenced 50 bp single-end on a HiSeq 2500 (Illumina). mRNA sample enrichment, library preparation, and sequencing were performed by the VBCF NGS Unit (https://www.vbcf.ac.at).

treatment_protocol: Fusion with organizer EB at D3 where specified

value: iPSC line reprogrammed at VBCF

value: wild-type

value: POLARIZED WITH 1%FGF8 ORGANIZER EB (OrEB)


title: H1FF polCA5_proximal

source_name: Human embryonic stem cells (hESC) H1 obtained from WiCell


title: iPSC 176/1 polCA6_distal


title: U2932_KLHL6_WT_OP9_DLL1_8h_biol_rep_2


title: iPSC 176/1 CONTROL4_segment3

value: UNTREATED


title: U2932_KLHL6_WT_OP9_DLL1_3h_biol_rep_1


title: BMDM, untreated, 0 hours, rep3

description:
batch2
BMDM_0h_rep3


title: U2932_KLHL6_WT_OP9_DLL1_3h_biol_rep_2


title: iPSC 176/1 polCA6_proximal


title: H9FF polCA4_distal

source_name: Human embryonic stem cells (hESC) H9 obtained from WiCell


title: H1FF polCA5_distal

value: Human embryonic stem cells (hESC) H1 obtained from WiCell


title: H9FF polCA4_medial

value: Human embryonic stem cells (hESC) H9 obtained from WiCell


title: H9FF CONTROL2_segment3


title: Adagrasib_Cetuximab_wave3_M52

extract_protocol:
Cells were lysed in TRI lysis reagent (Qiagen, #79306) according to the manufacturer's instructions. Total RNA was isolated with RNAeasy Mini Kit (Qiagen, #73404).
RNA-seq libraries were prepares using the TruSeq RNA Library Preparation Kit v2 according to manufacturer's instructions.

treatment_protocol: See samples section

value: colon carcinoma


title: H1FF polCA5_medial


title: Adagrasib_Cetuximab_wave3_M50


title: H9FF polCA4_proximal


title: Adagrasib_BI3406_wave3_D16


title: iPSC 176/1 CONTROL4_segment2


title: Adagrasib_BI3406_wave3_D14


title: iPSC 176/1 CONTROL4_segment1


title: U2932_KLHL6_WT_OP9_DLL1_8h_biol_rep_1

value: lymphoid


title: H1FF CONTROL3_segment3


title: Adagrasib_Cetuximab_wave2_M63


title: H1FF CONTROL3_segment2


title: H1FF CONTROL3_segment1


title: H9FF CONTROL2_segment2


title: Adagrasib_Cetuximab_wave2_M61


title: H9FF CONTROL2_segment1


title: plasma, T1D, S89

data_processing:
Data were analysed using QIAGEN GeneGlobe Data Analysis Center portal. Resulting reads were mapped referring to miRbase v21 and piRNABank using QIAGEN Gene Globe data analysis center software
Assembly: GRCh38/hg38
Supplementary files format and content: semicolon separated value file includes raw counts for each Sample

extract_protocol:
Total RNA extraction was performed from 200 µL of plasma through Serum/Plasma Norgen kit (cat. 55000, Thorold, ON L2V 4Y6, Canada)
Small RNA-derived cDNA libraries were prepared using QiaSeq miRNA library kit (cat. 331505, Qiagen)

value: plasma


title: plasma, T1D, S88


title: Adagrasib_Cetuximab_wave3_M51


title: Adagrasib_BI3406_wave3_D13


title: Adagrasib_Cetuximab_wave2_M64


title: Adagrasib_Cetuximab_wave3_M49


title: Adagrasib_Cetuximab_wave2_M62


title: Relapse_wave1_J294

value: Relapse


title: Relapse_wave1_J282


title: plasma, T1D, S85


title: Relapse_wave1_I261


title: Relapse_wave1_I244


title: plasma, T1D, S83


title: plasma, T1D, S87


title: Relapse_wave1_E137


title: Relapse_wave1_G208


title: Relapse_wave1_D116


title: plasma, T1D, S86b


title: Relapse_wave1_F174


title: Relapse_wave1_E138


title: plasma, T1D, S82


title: Relapse_wave1_A29


title: Relapse_wave1_F178


title: Relapse_wave1_D112


title: plasma, T1D, S81


title: plasma, T1D, S7


title: plasma, T1D, S80


title: Relapse_wave1_A27


title: Relapse_wave1_E149


title: plasma, T1D, S78


title: plasma, T1D, S79


title: Relapse_wave1_C70


title: Before_treatment_wave1_NR6


title: plasma, T1D, S74


title: plasma, T1D, S75


title: Before_treatment_wave1_NR4


title: plasma, T1D, S77


title: plasma, T1D, S71


title: plasma, T1D, S84


title: plasma, T1D, S76


title: Before_treatment_wave1_NR5


title: plasma, T1D, S73


title: NCI-H2122_Adagrasib_100mpk_TNO155_10mpk_48h_P65

value: lung carcinoma


title: plasma, T1D, S70


title: Before_treatment_wave1_NR2


title: plasma, T1D, S72


title: Relapse_wave1_D109


title: Before_treatment_wave1_NR1


title: Before_treatment_wave1_NR3


title: NCI-H2122_Adagrasib_100mpk_TNO155_10mpk_48h_P64


title: NCI-H2122_Adagrasib_100mpk_TNO155_10mpk_48h_P63


title: NCI-H2122_Adagrasib_100mpk_TNO155_10mpk_4h_O61


title: NCI-H2122_Adagrasib_100mpk_TNO155_10mpk_48h_P62


title: plasma, T1D, S6


title: plasma, T1D, S66


title: NCI-H2122_Adagrasib_100mpk_TNO155_10mpk_4h_O60


title: plasma, T1D, S69


title: plasma, T1D, S67


title: NCI-H2122_BI3406_50mpk_Adagrasib_100mpk_48h_M53


title: NCI-H2122_Adagrasib_100mpk_TNO155_10mpk_4h_O59


title: plasma, T1D, S64


title: plasma, T1D, S65


title: NCI-H2122_Adagrasib_100mpk_TNO155_10mpk_4h_O58


title: plasma, T1D, S63


title: plasma, T1D, S62


title: plasma, T1D, S61


title: plasma, T1D, S60


title: NCI-H2122_BI3406_50mpk_Adagrasib_100mpk_48h_M50


title: plasma, T1D, S5


title: NCI-H2122_BI3406_50mpk_Adagrasib_100mpk_4h_L49


title: NCI-H2122_BI3406_50mpk_Adagrasib_100mpk_4h_L46


title: plasma, T1D, S68


title: NCI-H2122_TNO155_10mpk_4h_I37


title: plasma, T1D, S59


title: plasma, T1D, S58


title: plasma, T1D, S56


title: NCI-H2122_TNO155_10mpk_4h_I34


title: plasma, T1D, S57


title: NCI-H2122_TNO155_10mpk_4h_I36


title: NCI-H2122_Adagrasib_100mpk_4h_F24


title: NCI-H2122_BI3406_50mpk_Adagrasib_100mpk_48h_M52


title: plasma, T1D, S55


title: NCI-H2122_Adagrasib_100mpk_4h_F25


title: plasma, T1D, S54


title: plasma, T1D, S50


title: NCI-H2122_Adagrasib_100mpk_4h_F23


title: plasma, T1D, S53


title: NCI-H2122_BI3406_50mpk_4h_C13


title: plasma, T1D, S4


title: plasma, T1D, S51


title: plasma, T1D, S49


title: NCI-H2122_BI3406_50mpk_4h_C12


title: NCI-H2122_Adagrasib_100mpk_4h_F22


title: NCI-H2122_BI3406_50mpk_4h_C11


title: plasma, T1D, S48


title: NCI-H2122_BI3406_50mpk_4h_C10


title: plasma, T1D, S47


title: NCI-H2122_TNO155_10mpk_4h_I35


title: plasma, T1D, S46


title: NCI-H2122_Vehicle_A4

value: Vehicle


title: plasma, T1D, S45b


title: plasma, T1D, S3


title: NCI-H2122_Vehicle_A2


title: plasma, T1D, S43


title: SW837_Adagrasib_100mpk_Cetuximab_20mpk_4h_X120


title: plasma, T1D, S44


title: NCI-H2122_Vehicle_A3


title: SW837_Adagrasib_100mpk_Cetuximab_20mpk_4h_X119


title: SW837_Adagrasib_100mpk_Cetuximab_20mpk_4h_X118


title: plasma, T1D, S42


title: plasma, T1D, S41


title: plasma, T1D, S39


title: SW837_Adagrasib_100mpk_Cetuximab_20mpk_24h_W115


title: SW837_Adagrasib_100mpk_Cetuximab_20mpk_4h_X117


title: plasma, T1D, S38


title: SW837_Adagrasib_100mpk_Cetuximab_20mpk_24h_W114


title: plasma, T1D, S35


title: plasma, T1D, S40


title: NCI-H2122_Vehicle_A5


title: SW837_BI3406_50mpk_Adagrasib_100mpk_48h_V109


title: plasma, T1D, S36b


title: SW837_Adagrasib_100mpk_Cetuximab_20mpk_24h_W111


title: plasma, T1D, S33


title: plasma, T1D, S32


title: SW837_BI3406_50mpk_Adagrasib_100mpk_4h_U104


title: plasma, T1D, S31


title: SW837_BI3406_50mpk_Adagrasib_100mpk_48h_V106


title: SW837_BI3406_50mpk_Adagrasib_100mpk_48h_V108


title: plasma, T1D, S34


title: plasma, T1D, S30


title: plasma, T1D, S29


title: plasma, T1D, S37


title: SW837_Adagrasib_100mpk_Cetuximab_20mpk_4h_X116


title: plasma, T1D, S28


title: SW837_BI3406_50mpk_Adagrasib_100mpk_4h_U102


title: SW837_Adagrasib_100mpk_Cetuximab_20mpk_24h_W112


title: plasma, T1D, S26


title: SW837_BI3406_50mpk_Adagrasib_100mpk_4h_U101


title: SW837_BI3406_50mpk_Adagrasib_100mpk_24h_T100


title: SW837_BI3406_50mpk_Adagrasib_100mpk_4h_U103


title: plasma, T1D, S27


title: plasma, T1D, S2


title: SW837_BI3406_50mpk_Adagrasib_100mpk_24h_T99


title: plasma, T1D, S25


title: SW837_BI3406_50mpk_Adagrasib_100mpk_24h_T98


title: SW837_BI3406_50mpk_Adagrasib_100mpk_24h_T96


title: plasma, T1D, S23


title: SW837_BI3406_50mpk_Adagrasib_100mpk_48h_V110


title: plasma, T1D, S24


title: SW837_BI3406_50mpk_Adagrasib_100mpk_48h_V107


title: SW837_Cetuximab_20mpk_48h_M65


title: SW837_Cetuximab_20mpk_48h_M64


title: plasma, T1D, S22


title: plasma, T1D, S21


title: plasma, T1D, S20


title: plasma, T1D, S19


title: SW837_Cetuximab_20mpk_48h_M62


title: SW837_Cetuximab_20mpk_48h_M61


title: plasma, T1D, S18


title: plasma, T1D, S1


title: SW837_Cetuximab_20mpk_4h_L58


title: SW837_Cetuximab_20mpk_4h_L57


title: SW837_Cetuximab_20mpk_4h_L60


title: SW837_Cetuximab_20mpk_4h_L59


title: plasma, T1D, S15


title: SW837_Cetuximab_20mpk_4h_L56


title: plasma, T1D, S16


title: plasma, T1D, S52


title: plasma, T1D, S14


title: SW837_Cetuximab_20mpk_24h_K55


title: SW837_Cetuximab_20mpk_24h_K53


title: SW837_Cetuximab_20mpk_24h_K54


title: plasma, T1D, S145b


title: plasma, T1D, S130b


title: plasma, T1D, S121b


title: SW837_Adagrasib_100mpk_48h_J49


title: SW837_Adagrasib_100mpk_48h_J48


title: SW837_Cetuximab_20mpk_48h_M63


title: plasma, T1D, S12b


title: SW837_Adagrasib_100mpk_48h_J47


title: SW837_Cetuximab_20mpk_24h_K52


title: SW837_Cetuximab_20mpk_24h_K51


title: SW837_Adagrasib_100mpk_4h_I45


title: plasma, T1D, S36


title: plasma, T1D, S17


title: SW837_Adagrasib_100mpk_4h_I44


title: plasma, T1D, S146


title: plasma, T1D, S45


title: plasma, T1D, S143


title: plasma, T1D, S13


title: plasma, T1D, S141


title: SW837_Adagrasib_100mpk_4h_I43


title: plasma, T1D, S86


title: plasma, T1D, S147


title: NCI-H2122_BI3406_50mpk_Adagrasib_100mpk_48h_M51


title: SW837_Adagrasib_100mpk_24h_H40


title: SW837_Adagrasib_100mpk_4h_I41


title: plasma, T1D, S142


title: SW837_Adagrasib_100mpk_24h_H38


title: SW837_Adagrasib_100mpk_4h_I42


title: plasma, T1D, S139


title: plasma, T1D, S140


title: SW837_Adagrasib_100mpk_24h_H36


title: plasma, T1D, S138


title: plasma, T1D, S137


title: plasma, T1D, S145


title: SW837_Adagrasib_100mpk_48h_J46


title: SW837_BI3406_50mpk_48h_D20


title: plasma, T1D, S12


title: SW837_BI3406_50mpk_48h_D19


title: plasma, T1D, S135


title: plasma, T1D, S144


title: plasma, T1D, S136


title: SW837_BI3406_50mpk_4h_C15


title: SW837_Adagrasib_100mpk_24h_H39


title: SW837_BI3406_50mpk_48h_D17


title: SW837_BI3406_50mpk_4h_C13


title: plasma, T1D, S132


title: plasma, T1D, S134


title: SW837_BI3406_50mpk_4h_C12


title: SW837_BI3406_50mpk_24h_B10


title: plasma, T1D, S133


title: plasma, T1D, S129


title: SW837_BI3406_50mpk_24h_B9


title: plasma, T1D, S130


title: plasma, T1D, S131


title: SW837_BI3406_50mpk_4h_C11


title: SW837_Vehicle_A5


title: SW837_BI3406_50mpk_24h_B6


title: plasma, T1D, S127


title: SW837_Adagrasib_100mpk_24h_H37


title: plasma, T1D, S128


title: SW837_Vehicle_A4


title: plasma, T1D, S126


title: plasma, T1D, S11


title: SW837_BI3406_50mpk_24h_B7


title: plasma, T1D, S125


title: SW837_Vehicle_A3


title: plasma, T1D, S124


title: SW837_BI3406_50mpk_48h_D18


title: plasma, T1D, S123


title: plasma, T1D, S120


title: SW837_Vehicle_A2


title: MCF7shLIFR 2D BR3

city: Nashville

first: Rachelle

last: Johnson

address: 2215B Garland Ave

institute: Vanderbilt University Medical Center

description:
24-MCF7shLIFR-2D-BR3
Biological replicate 3

data_processing:
Sequenced reads were mapped to hg38 genome by STAR (2.5.2a).
Mapped reads were assigned to Ensembl genes (v86) by HTSeq-Count with option -q -m intersection-nonempty -s no -i gene_id.
Differential expression analysis was performed by MultiRankSeq which was described in Guo Y, Zhao S, Ye F, Sheng Q, Shyr Y. MultiRankSeq: multiperspective approach for RNAseq differential expression analysis and quality control. Biomed Res Int. 2014;2014:248090. doi: 10.1155/2014/248090.
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Raw_RNAseq_counts_MCF7shLIFR_2D_samples.xlsx: Excel file includes raw counts for each Sample.
Supplementary_files_format_and_content: Excel file named MultiRankSeq_222324_vs_192021.html.diff.xlsx contains all of the analyses for these data. The processed data file provides relative gene expression values for DESeq, edgeR, and baySeq with adjusted p-values and Rank. The gene expression values provided indicate the fold change in gene expression in MCF7shLIFR cells relative to the MCF7NSC control cells.

source_name: Human MCF7 breast cancer cells

extract_protocol:
Cells were harvested in TRIzol and extracted per the manufacturer's instructions using phenol/chloroform.
The library was generated at the Stanford Functional Genomics Facility using the KAPA Stranded mRNA-Seq kit according to manufacturer's instructions.

treatment_protocol: The cells were grown in DMEM+10%FBS with no additional treatments. 16 hours prior to collection the cells were switched to DMEM+2%FBS containing approximately 15-30ul PBS.

tag: shRNA

value: shLIFR


title: MCF7NSC 2D BR1

description:
19-MCF7NSC-2D-BR1
Biological replicate 1

value: Non-silencing control


title: plasma, T1D, S118


title: MCF7shLIFR 2D BR2

description:
23-MCF7shLIFR-2D-BR2
Biological replicate 2


title: telencephalon_E14.5_female2

city: Sendai

first: Shohei

last: Ochi

state: Miyagi

address: 2-1, Seiryo-machi, Aoba-ku

department: Developmental Neuroscience

institute: Tohoku University Graduate School of Medicine

data_processing:
Sequencing and following data processing was performed by TAKARA BIO INC. Data processin was done using Genedata Profiler Genome (13.0.11)
Sequenced reads were mapped to GRCm38 (mm10) using STAR (v2.6.0c)
Annotation and read counts were done using Genedata Profiler Genome (13.0.11)
Assembly: GRCm38 (mm10)
Supplementary files format and content: xlsx format table file including raw counts and FPKM value for each sample

source_name: Telencephalon

extract_protocol:
total RNA was extracted using RNeasy Plus Mini Kit (QIAGEN).
cDNA was synthesized with TruSeq Stranded mRNA Sample Prep Kit (illumina) using XT-Auto System (Agilent). Subsequently, the generated libraries were then sequenced on HiSeq 2500 platform (illumine) with 100 bp paired end modules.

value: Telencephalon

tag: Sex

value: Female

value: WT

value: embryonic day 14.5


title: plasma, T1D, S122


title: plasma, T1D, S116


title: telencephalon_E14.5_male3

value: Male

tag: age


title: plasma, T1D, S115


title: MCF7NSC 2D BR3

description:
21-MCF7NSC-2D-BR3
Biological replicate 3


title: plasma, T1D, S121


title: MCF7NSC 2D BR2

description:
20-MCF7NSC-2D-BR2
Biological replicate 2


title: plasma, T1D, S119


title: MCF7shLIFR 2D BR1

description:
22-MCF7shLIFR-2D-BR1
Biological replicate 1


title: telencephalon_E11.5_female3

value: embryonic day 11.5


title: plasma, T1D, S114


title: telencephalon_E11.5_female2


title: telencephalon_E11.5_female1


title: plasma, T1D, S10


title: telencephalon_E14.5_female3


title: plasma, T1D, S109


title: telencephalon_E11.5_male2


title: plasma, T1D, S108


title: telencephalon_E14.5_male2


title: plasma, T1D, S113


title: plasma, T1D, S117


title: telencephalon_E14.5_female1


title: telencephalon_E14.5_male1


title: plasma, T1D, S112


title: Primary, DMSO, patient2

city: Solna

first: Tianyi

address: Bioclinicum NKS J5:20, Solnavägen 30

department: Oncology-Pathology

country: Sweden

institute: Karolinska Institute

data_processing:
bcl2fastq (v2.20.0.422) was used to demuliplex the fastq files.
umi_tools extract (v1.0) was then used to extract the barcodes/UMI and add them to the read names in the fastqs
Fastq files were aligned using STAR (v2.7.5b) to the human genome (GRCh38) obtained from Ensembl
The resulted bam files were then deduplicated using umi_tools dedup (v1.0)
Gene counting was then performed using featureCounts (v1.5.1) with Ensembl annotations (Homo_sapiens.GRCh38.101.gtf)
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files for all Samples

source_name: ovary

extract_protocol:
RNA was harvested using RNeasy mini plus kit (Qiagen). 1 ng of total RNA was used for the construction of sequencing libraries.
Libraries was prepared using QIAseq UPX 3’Transcriptome kit (Qiagen) according to manufacturer's protocol

value: ovary

value: Primary ovarian cells

tag: group

tag: concentration

value: DMSO


title: Primary, DMSO, patient3

tag: tissue

tag: cell line


title: plasma, T1D, S111


title: Primary, DMSO, patient1


title: plasma, T1D, S110


title: Primary, Untreated, patient3

value: MEDIA


title: plasma, T1D, S104


title: plasma, T1D, S102


title: telencephalon_E11.5_male1


title: telencephalon_E11.5_male3


title: plasma, T1D, S9


title: plasma, T1D, S105


title: plasma, T1D, S106


title: plasma, T1D, S103


title: Primary, MIX_1X, patient1


title: Primary, Untreated, patient2


title: plasma, T1D, S99


title: plasma, T1D, S101


title: plasma, T1D, S100


title: plasma, T1D, S97


title: plasma, T1D, S96


title: plasma, T1D, S107


title: Primary, MIX_10X, patient2


title: plasma, T1D, S98


title: Primary, MIX_10X, patient1


title: Primary, MIX_100X, patient2


title: plasma, T1D, S93


title: Primary, PFOS_1X, patient2


title: Primary, MIX_100X, patient3


title: plasma, T1D, S95


title: plasma, T1D, S91


title: plasma, T1D, S94


title: Primary, Untreated, patient1


title: Primary, PFOS_10X, patient3


title: Primary, MIX_100X, patient1


title: Primary, MIX_10X, patient3


title: Primary, PFOS_10X, patient1


title: Plasma,T1D,S114


title: Primary, MIX_1X, patient3


title: Primary, PFOS_1X, patient3


title: Primary, PFOS_100X, patient2


title: Plasma,T1D,S112


title: Primary, MIX_1X, patient2


title: plasma, T1D, S92


title: Primary, PFOS_1X, patient1


title: Plasma,T1D,S110


title: Primary, PCB180_1X, patient3


title: plasma, T1D, S90


title: plasma, T1D, S8


title: Plasma,T1D,S115


title: Plasma,T1D,S109


title: Primary, PFOS_10X, patient2


title: Primary, PCB180_10X, patient3


title: Plasma,T1D,S107


title: Primary, PCB180_10X, patient2


title: Plasma,T1D,S105


title: Primary, PFOS_100X, patient3


title: Plasma,T1D,S113


title: Primary, PCB180_100X, patient2


title: Plasma,T1D,S104


title: Primary, PFOS_100X, patient1


title: Plasma,T1D,S103


title: Primary, PCB180_1X, patient2


title: Plasma,T1D,S111


title: Plasma,T1D,S108


title: Primary, PCB156_1X, patient3


title: Plasma,T1D,S101


title: Primary, PCB180_100X, patient1


title: Plasma,T1D,S102


title: Primary, PCB180_100X, patient3


title: Plasma,T1D,S107b


title: Primary, PCB180_10X, patient1


title: Plasma,T1D,S100


title: Plasma,T1D,S106


title: Plasma,T1D,S99


title: Primary, PCB180_1X, patient1


title: Primary, PCB156_1X, patient2


title: Primary, PCB156_10X, patient3


title: Primary, PCB156_100X, patient3


title: Plasma,T1D,S98


title: Primary, PCB156_10X, patient1


title: Primary, PCB156_1X, patient1


title: Plasma,T1D,S97


title: Primary, PCB156_10X, patient2


title: Primary, PCB156_100X, patient1


title: Plasma,T1D,S96


title: Primary, DDE_1X, patient3


title: Primary, PCB156_100X, patient2


title: Plasma,T1D,S95


title: Plasma,T1D,S92


title: Plasma,T1D,S91


title: Primary, DDE_10X, patient2


title: Plasma,T1D,S93


title: Plasma,T1D,S89


title: Plasma,T1D,S94


title: Plasma,T1D,S90


title: Primary, DDE_1X, patient2


title: Primary, DDE_10X, patient3


title: Plasma,T1D,S88


title: Plasma,T1D,S87


title: Primary, DDE_10X, patient1


title: Plasma,T1D,S86


title: Primary, DDE_100X, patient3


title: Primary, HCB_1X, patient3


title: Plasma,T1D,S83b


title: Plasma,T1D,S84


title: Primary, DDE_100X, patient2


title: Plasma,T1D,S83


title: Primary, DDE_100X, patient1


title: Primary, HCB_10X, patient2


title: Plasma,T1D,S82


title: Plasma,T1D,S81


title: Primary, DDE_1X, patient1


title: PA1, DMSO, P341A

value: ovarian teratocarcinoma cell line PA1


title: Plasma,T1D,S77

value: plasma


title: Plasma,T1D,S76


title: PA1, DMSO, P340A


title: Plasma,T1D,S75


title: Primary, HCB_10X, patient1


title: Plasma,T1D,S80


title: PA1, Untreated, P341A


title: Plasma,T1D,S79


title: Primary, HCB_100X, patient2


title: Plasma,T1D,S71


title: Primary, HCB_100X, patient3


title: PA1, MIX_1X, P340A


title: PA1, MIX_1X, P339A


title: Plasma,T1D,S78


title: Primary, HCB_100X, patient1


title: Plasma,T1D,S67


title: Plasma,T1D,S66


title: PA1, Untreated, P340A


title: Plasma,T1D,S73


title: Plasma,T1D,S63


title: Plasma,T1D,S85


title: Plasma,T1D,S62


title: PA1, DMSO, P339A


title: Plasma,T1D,S61


title: Primary, HCB_1X, patient2


title: Primary, HCB_1X, patient1


title: Plasma,T1D,S72


title: Plasma,T1D,S60


title: Plasma,T1D,S59


title: PA1, PFOS_10X, P341A


title: PA1, Untreated, P339B


title: Plasma,T1D,S70


title: PA1, PFOS_1X, P341B


title: Plasma,T1D,S68


title: PA1, MIX_10X, P341A


title: Plasma,T1D,S69


title: PA1, PFOS_10X, P339A


title: Plasma,T1D,S55


title: PA1, PFOS_100X, P340A


title: PA1, MIX_10X, P340A


title: Plasma,T1D,S54b


title: PA1, MIX_10X, P339A


title: PA1, PFOS_100X, P339A


title: Plasma,T1D,S74


title: Plasma,T1D,S65


title: PA1, MIX_100X, P341A


title: Plasma,T1D,S64


title: Plasma,T1D,S54


title: PA1, MIX_100X, P340A


title: PA1, MIX_1X, P341A


title: PA1, PCB180_1X, P339A


title: PA1, MIX_100X, P339A


title: Plasma,T1D,S51


title: PA1, PCB180_10X, P341A


title: PA1, PFOS_1X, P340A


title: PA1, PFOS_1X, P339A


title: PA1, PCB180_10X, P340A


title: Plasma,T1D,S58


title: Plasma,T1D,S57


title: PA1, PCB180_10X, P339A


title: Plasma,T1D,S56


title: PA1, PCB180_100X, P339A


title: PA1, PFOS_100X, P341A


title: PA1, PFOS_10X, P340A


title: PA1, PCB180_1X, P341A


title: Plasma,T1D,S53


title: PA1, PCB156_1X, P339A


title: PA1, PCB180_1X, P340A


title: Plasma,T1D,S43


title: Plasma,T1D,S52


title: Plasma,T1D,S41


title: Plasma,T1D,S50


title: Plasma,T1D,S47


title: Plasma,T1D,S49b


title: PA1, PCB156_1X, P341A


title: Plasma,T1D,S49


title: Plasma,T1D,S39


title: PA1, PCB180_100X, P340A


title: Plasma,T1D,S48


title: PA1, PCB180_100X, P341A


title: Plasma,T1D,S45


title: Plasma,T1D,S46


title: PA1, PCB156_1X, P340A


title: PA1, PCB156_10X, P341A


title: Plasma,T1D,S44


title: Plasma,T1D,S42


title: PA1, DDE_1X, P341A


title: PA1, PCB156_10X, P339A


title: PA1, PCB156_10X, P340A


title: Plasma,T1D,S35


title: PA1, PCB156_100X, P340A


title: Plasma,T1D,S34


title: PA1, PCB156_100X, P341A


title: PA1, DDE_10X, P340A


title: Plasma,T1D,S38


title: PA1, DDE_10X, P341A


title: Plasma,T1D,S32


title: PA1, PCB156_100X, P339A


title: PA1, DDE_100X, P341A


title: Plasma,T1D,S40


title: Plasma,T1D,S33


title: Plasma,T1D,S36


title: PA1, DDE_1X, P340A


title: Plasma,T1D,S28


title: PA1, HCB_1X, P341A


title: Plasma,T1D,S31


title: PA1, DDE_1X, P339A


title: PA1, DDE_100X, P340A


title: 42hpi, pBOMB, UnInduced, rep2

city: Irvine

first: Syed

middle: Meraj Azhar

last: Rizvi

address: University of California Irvine

department: Microbiology and Molecular Genetics

country: India

institute: University of California Irvine

description: 32 hours infection

data_processing:
The intensities of the spots on the images and the base calls are computed directly during the run using Illumina’s Real Time Analysis (RTA) software installed on a computer located in the UCI-GHTF.
Reads were mapped to C. trachomatis L2 434/Bu genome and reads were counted for annotated genes on Qiagen CLC Genomics Workbench (version 21.0.5) software with high stringency settings (mismatch cost 2, and insertion and deletion cost 3, length and similarity fraction 0.8 each, maximum number of hits for a read to 10, and minimum read count fusion table to 5).
Assembly: GCA_000068585.1
Supplementary files format and content: Each processed data file corresponding to the libraries is an Excel (.xlsx) file containing name of C. trachomatis genes, chromosome, region, expression value, TPM value, RPKM value, gene length, unique gene reads, and total gene reads

organism: Chlamydia trachomatis

source_name: HeLa

growth_protocol: DMEM, 10% fetal bovine serum. Cells were cultured at 37C at 5% CO2.

extract_protocol:
C. trachomatis infected HeLa were resuspended in TRIzol (300 ul/ well in 24 well plate). After centrifugation, the aqueous layer containing the total RNA was loaded on the Qiagen column and supplier instructions were followed hereafter. RNA was DNase treated on the column and eluted in MQ water. After RNA extraction, the samples were analyzed by Qubit to check for any degradation of the RNA. The yield of the RNA samples was measured on a Qubit.
RNASeq library prepared using Zymo-seq RiboFree Total RNA Library Kit by Zymo Research, with 10ng of total RNA

value: HeLa

tag: cell type

value: Epithelial cells

value: Transformed with pBOMB4


title: Plasma,T1D,S30


title: PA1, DDE_10X, P339A


title: Plasma,T1D,S29


title: Plasma,T1D,S27


title: PA1, DDE_100X, P339A


title: PA1, HCB_10X, P341A


title: PA1, HCB_1X, P339A


title: 36hpi, pBOMB, UnInduced, rep2

description: 32 hours infection


title: PA1, HCB_10X, P339A


title: Plasma,T1D,S26


title: PA1, HCB_100X, P341A


title: PA1, HCB_1X, P340A


title: 36hpi, pBOMB, UnInduced, rep1

description: 32 hours infection


title: PA1, HCB_100X, P340A


title: Plasma,T1D,S24


title: Plasma,T1D,S25


title: PA1, HCB_10X, P340A


title: Tumor single cell multiome ATAC

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

institute: Japanese Foundation for Cancer Research

description: 10x Genomics

library_source: genomic single cell

data_processing:
All analysises were performed using Cell Ranger Arc software 2.0.1
Assembly: mm10
Supplementary files format and content: h5 matrix and tab-separated fragment files

source_name: primary

extract_protocol:
GNPs, PNCs, and tumor cells were isolated from the cerebellum of Ptch1- Atoh1EGFP mice at P7, 6 weeks, and adulthood using percoll gradient centrifugation, respectively. Nuclei isolation was performed according to the manufacturer’s protocol (CG000366 Rev C, 10x Genomics). Of note, the incubation with the lysis buffer was optimized to 3 minutes. Targeted Nuclei Recovery was 5000 or 10000, depending on the number of isolated nuclei.
Single Cell Multiome ATAC + Gene Expression; Library preparation was performed according to the manufacturer’s protocol (CG000338 RevE, 10x Genomics).

value: primary

value: medulloblastoma


title: 28hpi, pBOMB, UnInduced, rep2

description: 28 hours infection


title: PNC single cell multiome RNA

description: 10x Genomics

molecule: cytoplasmic RNA

value: preneoplastic cells


title: Tumor single cell multiome RNA

description: 10x Genomics


title: KGN, DMSO, P16A

value: granulosa cancer cell line KGN


title: PNC single cell multiome ATAC

description: 10x Genomics


title: KGN, DMSO, P13A

value: WT


title: 28hpi, pBOMB, UnInduced, rep1

description: 28 hours infection


title: Plasma,T1D,S23


title: PA1, HCB_100X, P339A


title: 32hpi, pBOMB, UnInduced, rep2

description: 28 hours infection


title: Plasma,T1D,S22


title: 42hpi, pBOMB, UnInduced, rep1

description: 32 hours infection


title: 32hpi, pBOMB, UnInduced, rep1

description: 28 hours infection


title: Plasma,T1D,S21


title: Ptch1GNP single cell multiome RNA

description: 10x Genomics

value: granule neuron progenitors


title: 24hpi, pBOMB, UnInduced, rep2

description: 24 hours infection


title: Ptch1GNP single cell multiome ATAC

description: 10x Genomics


title: KGN, Untreated, P16A


title: Plasma,T1D,S37


title: KGN, DMSO, P12B


title: Plasma,T1D,S20


title: 24hpi, pBOMB, UnInduced, rep1

description: 24 hours infection


title: 20hpi, pBOMB, UnInduced, rep2

description: 20 hours infection


title: Plasma,T1D,S19


title: KGN, Untreated, P13A


title: Tumor H3K27Ac 2

data_processing:
Library strategy: Cut&Tag
Fastq files were generated by RTA in Illumina NextSeq 550.
Adaptor sequence were trimmed by Skewer
Reads were mapped to mm10 genome by bowtie2
Peak call was performed by MACS2
Assembly: mm10
Supplementary files format and content: narrow peak data

extract_protocol:
GNPs, PNCs and tumor cells were isolated from P7, P28 and adult cerebellum by percoll gradient centrifugation, respectively. These isolated 1 x 10^5 cells were directly subjected to CUT & Tag library preparation.
CUT & Tag was performed according to the online protocol from EpiCypher


title: Tumor H3K27Ac 1


title: Tumor H3K27Ac 3


title: Plasma,T1D,S17


title: 20hpi, pBOMB, UnInduced, rep1

description: 20 hours infection


title: 16hpi, pBOMB, UnInduced, rep2

description: 16 hours infection


title: Plasma,T1D,S16


title: KGN, Untreated, P12A_P3


title: PNC H3K27Ac 3


title: Plasma,T1D,S15


title: KGN, MIX_1X, P11A


title: KGN, MIX_1X, P14A


title: 16hpi, pBOMB, UnInduced, rep1

description: 16 hours infection


title: 8hpi, pBOMB, UnInduced, rep2

description: 8 hours infection


title: KGN, MIX_10X, P14B


title: PNC H3K27Ac 2


title: Plasma,T1D,S19b


title: 8hpi, pBOMB, UnInduced, rep1

description: 8 hours infection


title: Plasma,T1D,S18


title: GNP H3K27Ac 3


title: Plasma,T1D,S13


title: GNP H3K27Ac 2


title: 4hpi, pBOMB, UnInduced, rep2

description: 4 hours infection


title: KGN, MIX_10X, P10A


title: VDR ATAC siNfib 3

data_processing:
Fastq files were generated by RTA in Illumina NextSeq 550.
Adaptor sequence were trimmed by Skewer
Reads were mapped to mm10 genome by bowtie2
PCR de-duplicate was performed by Picard
Peak call was performed by MACS2
Assembly: mm10
Supplementary files format and content: peak summit data

source_name: cell line

extract_protocol:
To isolate GNP and hyperplasia cells from P7 and P28 Atoh1EGFP cerebella, the tissues were dissociated, followed by percoll gradient centrifugation as previously described. For tumor cell isolation, tumor-bearing cerebella was dissociated with Trypsin/DNase and filtrated though 40 μm cell strainer (CORNING). Subsequently, the cells were suspended in cold DPBS containing 1% BSA for cell sorting of EGFP positive cells with FACSAriaTM sorters (BD Biosciences).
Libraries were prepared with the Omni-ATAC protocol.

value: cell line

value: VDR

value: siNfib 3


title: GNP H3K27Ac 1


title: Plasma,T1D,S12


title: KGN, MIX_100X, P14A

value: ovary


title: KGN, MIX_1X, P10A


title: PNC H3K27Ac 1


title: Plasma,T1D,S11


title: Medaka_SEDL Knockout #2

city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

institute: Tigem

description: Transcriptome profile of a wild type 40 Oryzias latipes (Medaka) embryo KO for SEDL, biological rep2

data_processing:
Sequence reads were trimmed using bbduk software(https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/usage-guide/) (bbmap suite 37.31) to remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6) and then aligned on mm10 reference sequence using STAR
Genome_build: oryLat2
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

organism: Oryzias latipes

source_name: Embryo

growth_protocol: The Cab-strain of medaka fish (Oryzias latipes) was maintained as described in Avellino et al., 2013. Embryos were staged according to the method proposed by Iwamatsu (Iwamatsu, 2004). All studies on fish were conducted in strict accordance with the institutional guidelines for animal research and approved by the Italian Ministry of Health; Department of Public Health, Animal Health, Nutrition and Food Safety in accordance to the law on animal experimentation (D.Lgs. 26/2014). Furthermore, all animal treatments were reviewed and approved in advance by the Ethics Committee at the TIGEM Institute, (Pozzuoli (NA), Italy).

extract_protocol:
RNA was quantified and mixed at 10ng/µl
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NovaSeq500 (Illumina) with a read length of 100 bp

tag: developmental stage

value: Stage 40

value: embryo

tag: gender

value: not determined


title: Medaka_SEDL Knockout #3

description: Transcriptome profile of a wild type 40 Oryzias latipes (Medaka) embryo KO for SEDL, biological rep3


title: 4hpi, pBOMB, UnInduced, rep1

description: 4 hours infection

tag: treatment


title: Plasma,T1D,S14

value: plasma


title: VDR ATAC siNfib 2

value: siNfib 2


title: Plasma,T1D,S9


title: KGN, MIX_100X, P10A


title: KGN, MIX_100X, P11A


title: Plasma,T1D,S10


title: Medaka_SEDL Knockout #1

description: Transcriptome profile of a wild type 40 Oryzias latipes (Medaka) embryo KO for SEDL, biological rep1


title: VDR ATAC siNfib 1

value: siNfib 1


title: Plasma,T1D,S8


title: Medaka_Control #4

description: Transcriptome profile of a wild type 40 Oryzias latipes (Medaka) embryo wild type, biological rep3


title: KGN, PFOS_1X, P14A


title: Plasma,T1D,S7


title: KGN, MIX_10X, P11A


title: KGN, PFOS_1X, P11A


title: VDR ATAC siNfia 3

value: siNfia 3